QIAGEN CLC Genomics

Accelerating Viral Construct Design and QC with QIAGEN CLC Genomics Workbench

Wed, 22 Apr 2026 00:41:26 GMT

Viral constructs are essential tools for gene therapy, vaccine development and advanced cell engineering workflows. QIAGEN CLC Genomics Workbench has the tools to streamline each stage of construct development, from in silico design to resequencing analysis and adventitious agent detection.

In this webinar, you will learn how to build custom viral variants, verify construct integrity using NGS data and ensure manufacturing safety through sensitive, reproducible contaminant screening.

Design and build custom viral constructs using intuitive sequence editing, annotation and assembly tools, supporting rapid prototyping and iterative engineering.
Analyze resequencing data for construct verification, including reference-based mapping, mutation profiling, structural variant detection and quality control (QC) reporting to confirm construct fidelity.
Detect and characterize adventitious agents during manufacturing using metagenomic pipelines, taxonomic classification tools and cross‑contamination analysis within CLC Genomics Workbench.

Population Genetics in an Era of Genomic Health

Fri, 27 Mar 2026 13:44:42 GMT

Advances in genomic medicine hold enormous promise, but that promise cannot be fully realized without greater diversity in research and clinical application.

In this webinar, Eimear Kenny will discuss how population genetics can drive more accurate, equitable genomic health by expanding representation in genomic studies and databases. Drawing on work from her group at the Icahn School of Medicine at Mount Sinai, she will highlight efforts in expanding the understanding of human genomic diversity by prioritizing populations underrepresented in genomics, developing and sharing computational tools that improve precision across diverse populations, and uncovering disease-related genetic architectures shaped by demographic history.

In this webinar, attendees will:

Learn how her research group is expanding diversity in large-scale genomic databases and integrating new models of genomic medicine into routine clinical care to ensure insights translate into real-world practice
Explore why inclusivity, methodological innovation and diverse populations are essential to advancing genomic health, improving patient care and promoting health equity

Single-cell RNA-seq, cell hashing and spatial transcriptomics

Thu, 26 Mar 2026 15:36:07 GMT

In this training, you will learn how to analyze and interpret your own single cell RNA-seq data using QIAGEN CLC Genomics Workbench starting with either FASTQ or matrix files.

Using CLC Genomics Workbench, you will learn how to perform secondary analysis on your single cell RNA-seq data. Specifically, you will learn how to:

• Import your raw FASTQ or processed cell-matrix files.

• Use pre-configured but customizable pipelines/workflows for single cell RNA-seq data.

• Generate high resolution visuals and other files from your analysis for publications and biopharmaceutical discoveries.

o Dimension reduction (UMAP, t-SNE) plots

o Differential expression table for clusters, cell types, or combination of both

o Heat map

o Dot plots

o Violin plots

• Learn how to use “Create Cell Annotations from Hashtags” for cell hashing (i.e., CITE-seq).

• Dive into spatial transcriptomic analysis, the latest feature in the single cell RNA-seq module.

NGS for GMP compliance: New guidelines, new tools

Mon, 23 Mar 2026 13:16:49 GMT

The updated ICH Q5A(R2) guidelines recommend next-generation sequencing (NGS) as the preferred approach for detecting adventitious agents. From cell line development and viral clearance studies to contamination tracing and product characterization, NGS-based tests outperform older assays in efficacy, sensitivity and reproducibility. This forms the basis for implementation by leading regulatory authorities, including the FDA, EMA, PMDA, and MFDS, signaling a global shift in biosafety testing.

Ensure easy compliance with these new directives by using a robust, computer systems validation (CSV)-friendly software platform that supports transparency and traceability throughout your biologics production pipeline.

You will learn

- The impact of current guidelines, including ICH Q5A(R2), FDA 21 CFR Part 11 and European Pharmacopeia Chapter 2.6.41 on biologics production
- Key requirements on data integrity, audit trails, user authentication and more, for setting up GMP environments
- How QIAGEN CLC Genomics Workbench and Server support achieving GMP compliance

Long reads analysis using QIAGEN CLC Genomics Workbench

Thu, 26 Feb 2026 17:50:30 GMT

This webinar will introduce you to the Long Read Support plugin for Oxford Nanopore and PacBio sequencing reads in QIAGEN CLC Genomics Workbench.

Learn how to:

- Download and install needed plugins
- Import data required for the analysis
- Perform long read de novo assembly
- Map reads to a reference and visualize an assembly
- Use BLAST to investigate the contigs
- Use additional long read tools: polish with short reads, structural variant calling
- Use genome finishing tools: analyze and assemble contigs
- Use analytical tools: RNA-seq analysis for long reads, classify long read amplicons for metagenomics

Associating metadata with samples in CLC

Mon, 09 Feb 2026 13:13:19 GMT

In this video, we demonstrate the import and association of metadata with sample files.

https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Metadata.html

How to view overlapping genes in a Venn Diagram using the synchronized table...

Mon, 09 Feb 2026 13:09:01 GMT

In this video, we demonstrate how to view details of specific data points in plot views using the synchronized table view. See how you can easily access the list of genes that overlap in a Venn diagram for RNA-seq. This functionality is also available for other types of plots like track lists, expression browsers and volcano plots, to name a few.

Introduction to Fork Collections

Mon, 09 Feb 2026 13:00:33 GMT

Starting with CLC version 26, workflow control can be simplified using fork collections.

https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Fork.html#SECTION001425230000000000000

Single-cell RNA-seq analysis made easy - February 24

Wed, 28 Jan 2026 21:53:39 GMT

Single-cell gene expression analysis starting from either FASTQ or expression data is now supported by QIAGEN CLC Genomics Workbench Premium, the scalable cross-platform desktop software for NGS data analysis. In this webinar, we will re-analyze data from a study on transcriptional profiling of the mouse heart (Skelly et al., 2018), starting from FASTQ and ending with detecting sexually dimorphic genes within different cell types.

Reference: Skelly, Daniel A., et al. (2018) Single-cell transcriptional profiling reveals cellular diversity and intercommunication in the mouse heart. Cell reports 22.3: 600-610.

Topics covered:
• Introduction to the QIAGEN CLC Genomics Workbench
• Generation of t-SNE and UMAP plots, starting from raw FASTQ read files
• Automated annotation of cell types using QIAGEN’s cell type classifier
• Detection of differentially expressed genes in different cell types in a case vs. control setting

RNA-seq data analysis using QIAGEN CLC Genomics Workbench

Mon, 26 Jan 2026 13:52:53 GMT

For your RNA-seq data, you will learn how to:

• Import FASTQ files, cell matrix files and metadata

• Download and/or import reference and annotations files

• Map reads to a reference genome

• Generate gene and transcript counts

• QC reports displaying % mapped reads etc.

• Generate visualizations of results, such as heatmaps, differential expression tables, PCA/PCOA plots, Venn diagrams, Sankey plot and more

• Easily customize RNA-seq workflows

• Export publication-quality graphics, tables and reports

Per audience request

• Send differential expression tables to QIAGEN Ingenuity Pathway Analysis directly from QIAGEN CLC Genomics Workbench to analyze and interpret relevant pathways

Advance workflow constructions using the CLC Genomics workbench

Thu, 22 Jan 2026 09:56:38 GMT

In today’s session, we’ll explore the major enhancements to the workflow system that greatly improve usability, flexibility, and authoring efficiency. We’ll look at new grouping and branching features that simplify complex workflow design, updated editor tools that make navigation and validation easier, and improvements that streamline adding, managing, and reusing workflow components. We’ll also cover the newly workflow-enabled tools and how workflows can now be installed even when some tools are unavailable – making collaboration and sharing smoother than ever.

• Overview of major workflow system enhancements

• New grouping and branching features for easier design

• Streamlined workflow editor with improved navigation and validation

• Faster, more consistent workflow creation and reuse

• Newly workflow-enabled tools and improved installation flexibility

Investigating genomic variants using QIAGEN CLC Genomics Workbench, QCI...

Thu, 08 Jan 2026 10:40:11 GMT

Discovery of new genes implicated in hereditary diseases or cancer progression is challenging and advancing rapidly with an increase in the amount of cohort data to analyze from next generation sequencing (NGS) data to associations between gene variants and diseases, and finally to biological mechanisms of these gene variants. Combining QIAGEN CLC Genomics Workbench, QCII-T, and IPA, scientists can analyze sequencing data obtained from a variety of NGS technologies, annotate gene variants using the world’s most comprehensive and up-to-date curated scientific evidence, and find biological connections in gene variants with manually curated scientific findings. Get valuable and reliable insights for your research project and speed up your discoveries by using a streamlined NGS analysis workflow.

In this webinar, attendees will have the opportunity to:

1. Learn how to import whole genome or exome sequencing data into QIAGEN CLC Genomics Workbench and use the ultra-fast LightSpeed Module that delivers end-to-end NGS FASTQ to VCF pipeline;

2. Explore capabilities in QCII-T which can enable scientists to accelerate discoveries from hereditary or tumor cohort analyses to find associations between gene variants and diseases;

3. Learn how to use IPA and its manually curated content among other integrated scientific evidence to uncover novel biological mechanisms underlying these gene variants.

Single Cell RNA-Seq and Spatial Transcriptomics

Thu, 13 Nov 2025 09:15:18 GMT

In this webinar, the speaker will cover how to simplify your single cell RNA-seq analysis with biologist-friendly point and click tools.

• Generate high-resolution visuals and other files from your analysis for publications and biopharmaceutical discoveries

• Generate dimension reduction (UMAP, t-SNE) plots to understand differences between cell clusters/experimental conditions

• Identify and study clusters and cell types specific biomarkers using differential expression tables, gene expression heat maps, dot plots and violin plots

• Generate desired cell annotations using hashtags

• Visualize and investigate spatial transcriptomics plot using your Cell Ranger output to better understand cellular organization and generate hypothesis

• Use preconfigured but customizable pipelines/workflows for single-cell RNA-seq data

The increasing Accessibility of Cell Therapy, Gene Therapy, and Clinical...

Thu, 06 Nov 2025 17:43:56 GMT

Precision medicine is rapidly transforming healthcare, and one of the most significant accelerators of its progress has been the dramatic reduction in cost. In this webinar, we explore how innovations in genomics and biotherapeutics are making advanced, personalized healthcare more accessible and affordable than ever before. Dr. George M. Church will examine how the cost of whole genome sequencing has been reduced from $3 billion per haploid genome—previously unusable in clinical settings—to just $300 per phased diploid genome today. We’ll also look at the economics behind cell therapy, such as blood transfusions (now as low as $200), and gene therapy technologies like mRNA vaccines (available for as little as $30).

Mapping the Human Body One Cell at a Time

Wed, 05 Nov 2025 16:13:15 GMT

The 37 trillion cells of the human body have a remarkable array of specialized functions and must cooperate in time and space to construct a functioning human.

In this webinar, Sarah Teichmann, professor of stem cell medicine at the University of Cambridge and co-founder and co-leader of the International Human Cell Atlas Consortium, discusses how her lab harnesses cutting-edge single-cell and spatial genomics to better understand this cellular diversity — specifically, how distinct microenvironments regulate cell identity.

The lab’s spatial atlas of the adult human heart includes the first comprehensive map of the conduction system, and it harnessed the unique molecular signature of the very rare pacemaker cells to make predictions about potential drug activities. Moving from the single organ to the systems level, Teichmann’s team revealed the context-specific and context-agnostic features of the vasculature across the body.

Finally, the team has taken cell atlases into 3D and 4D with its thymus atlases. Studying thymus development uncovered the rules of T-cell identity, which Teichmann’s team then harnessed in the dish to engineer T cells from thymic organoids. The lab also used advanced spatial and computational methods to map T-cell development to a continuous tissue axis, identifying the key spatial and temporal features of this crucial developmental trajectory.

Single-cell RNA-seq, cell hashing and spatial transcriptomics

Fri, 24 Oct 2025 09:52:45 GMT

In this training, you will learn how to analyze and interpret your own single cell RNA-seq data using QIAGEN CLC Genomics Workbench starting with either FASTQ or matrix files.

Using CLC Genomics Workbench, you will learn how to perform secondary analysis on your single cell RNA-seq data. Specifically, you will learn how to:

Import your raw FASTQ or processed cell-matrix files.
Use pre-configured but customizable pipelines/workflows for single cell RNA-seq data.
Generate high resolution visuals and other files from your analysis for publications and biopharmaceutical discoveries.
- Dimension reduction (UMAP, t-SNE) plots
- Differential expression table for clusters, cell types, or combination of both
- Heat map
- Dot plots
- Violin plots
Learn how to use “Create Cell Annotations from Hashtags” for cell hashing (i.e., CITE-seq).
Dive into spatial transcriptomic analysis, the latest feature in the single cell RNA-seq module.

16S/18S/ITS sequencing analysis using CLC Genomics Workbench

Thu, 23 Oct 2025 16:07:15 GMT

QIAGEN CLC Microbial Genomics Module provides tools and workflows for a broad range of bioinformatics applications, including microbiome analysis, isolate characterization, functional metagenomics and antimicrobial resistance characterization. The module supports the analysis of bacterial, viral and eukaryotic (fungal) genomes and metagenomes.

This training will be focused on amplicon-based taxonomic profiling (16S/18S/ITS sequencing OTU clustering). The trainer will cover:

Overview of different tools within QIAGEN CLC Microbial Genomics Module and supported research areas
For taxonomic profiling:
- Importing data
- Utilization of metadata
- Downloading and managing references
- Walk through of OTU clustering workflow (analytical pipeline)
- Downstream processing of abundance tables
- Creating and exporting high-quality graphics

Somatic variant detection with Twist Oncology and QIAGEN CLC

Tue, 07 Oct 2025 12:41:35 GMT

See how highly sensitive somatic detection of classic tumor reference samples is made possible through the Twist Oncology - DNA CGP Panel™ combined with downstream analysis using QIAGEN® CLC Genomics Workbench.

What is the Twist Oncology - DNA CGP Panel?

It is a panel from Twist Biosciences® that is designed for the comprehensive genomic profiling (CGP) of solid tumors to find pathogenic variants. It also supports the scoring of microsatellite instability (MSI) and tumor mutational burden (TMB).

What is QIAGEN CLC Genomics Workbench?

A powerful all-in-one analysis and visualization toolkit, it is software filled with various tools and workflows tailored to next-generation sequencing (NGS) data, including data from a wide range of resequencing panel designs.

Batch Mode in CLC

Mon, 06 Oct 2025 15:16:09 GMT

In this video we introduce sample batching using CLC tools. This can be helpful when you need to perform the same analysis on a large number of files. Also see this manual page for more details:

https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Batch_processing.html

Analyzing Samples with Multiple Inputs in CLC

Mon, 06 Oct 2025 15:14:44 GMT

This video demonstrates how to analyze multiple input files per sample using batch mode. Please also see this FAQ page for more details:

How can I run a batch job with multiple libraries for each sample?

Comparing Analysis Parameters using the History View in CLC

Mon, 06 Oct 2025 15:13:47 GMT

The history view keeps track of what tools and parameters were used to generate results in CLC. This video shows how the history view can be used to compare two different analyses when the results are unexpected.

Details about the history view can be found on this manual page:

https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=History_Element_Info_views.html

MyCLC Overview

Mon, 06 Oct 2025 15:13:00 GMT

This video provides a quick introduction to myCLC. If you do not already have access to myCLC Please contact bioinformaticslicense@qiagen.com

Also, check out these FAQ pages:

What is myCLC?

How can I get access to myCLC?

How can I find information about my CLC licenses?

How can I add someone as a technical contact to myCLC?

How can I view information for another myCLC account?

How to Create a Track list in CLC

Mon, 06 Oct 2025 15:12:19 GMT

In this video you can learn how to import tracks and create a track list in CLC. Track lists enable users to view multiple track elements at once. Track lists also feature an interactive link between the table view and the plot view.

Use track lists to browse genomic features, zoom into regions of interest, visualize read mappings, inspect variants, and more. Please also see this manual page for more details:

https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Track_lists.html

Create publication-ready volcano plots for RNA-sq data using CLC genomics...

Mon, 06 Oct 2025 15:11:15 GMT

This video shows how to customize volcano plots in CLC Genomics Workbench. Check out these tutorials for more RNA-seq related topics:

https://digitalinsights.qiagen.com/support/tutorials/#:~:text=Expression%20and%20fusions

Scale up NGS bioinformatics analysis throughput with QIAGEN CLC Genomics...

Fri, 03 Oct 2025 12:11:29 GMT

More and more biopharma and academic groups are looking to process a large number of samples simultaneously or for a quicker turnaround time. This webinar will introduce a flexible and powerful setup for running your NGS sequence analyses through servers or Amazon Web Services (AWS). See how QIAGEN CLC Genomics Workbench can be used to customize workflows and send analyses for batch execution. We will also highlight analysis automation solutions, use of third-party dockers, audit trails and user management – all of which are available within the CLC Genomics Server software.

You will learn to:

• Customize template workflows to meet your NGS analysis requirements

• Set up a CLC Genomics Cloud environment on AWS

• Submit workflows to run on internal servers or AWS and retrieve results from these analyses

• Use third-party dockers and automate workflow execution

RNA-Seq Data Analysis and Interpretation using QIAGEN CLC Genomics Workbench...

Fri, 03 Oct 2025 09:27:56 GMT

The increasing adoption of next-generation sequencing in many fields has made RNA-seq data analysis and interpretation essential skills for researchers. In this webinar, discover how you can effortlessly process FASTQ files with QIAGEN CLC Genomics Workbench (CLC). Next, you will import differential expression results directly into QIAGEN Ingenuity Pathway Analysis (IPA) for downstream analysis – enabling a smooth path from data to discovery.

You will learn how to:

• Use CLC to map reads to a reference genome, generate gene/transcript counts and QC reports

• Use CLC to visualize results, such as heatmaps, differential expression tables, PCA/PCOA plots, Venn diagrams and more

• Use IPA to identify enriched canonical pathways, diseases and biological functions and predicted upstream regulators

• Use IPA to compare your analysis results to over 200,000 analyses curated from public ‘omics datasets – including your own projects – to find similarities and differences in pathways, upstream regulators and diseases

Discover Microbial Functional Insights with QIAGEN CLC Genomics Workbench

Thu, 02 Oct 2025 17:04:30 GMT

Join us for an in-depth webinar showcasing the discovery of functional insights in microbial communities using QIAGEN CLC Genomics Workbench tools. Ideal for microbiologists, bioinformaticians and researchers aiming to uncover functional signatures in microbial communities and drive data-driven discoveries, you will learn how to perform a comprehensive whole metagenome functional analysis, from raw NGS data to functional profiling and visualization.

Whether you are working with experimental or clinical samples, this session will equip you with a robust, scalable pipeline for comparative functional metagenomics.

Learn how to:

• Import and prepare raw NGS data

• Assemble metagenomes into contigs

• Map reads and bin pangenomes by sequence

• Identify genes and coding DNA sequences (CDS)

• Annotate functional elements using Gene Ontology (GO) and Pfam domains

• Build functional profiles to explore diversity

• Visualize and analyze functional differences across sample groups

Workflow construction and customization using QIAGEN CLC Genomics Workbench

Fri, 19 Sep 2025 09:38:36 GMT

QIAGEN CLC Genomics Workbench allows easy construction and customization of variety of bioinformatic analysis workflows such as DNA-seq, RNA-seq, De Novo Assembly and more. Per feedback received, this session will focus on

• A quick and brief introduction to CLC Genomics Workbench

• How to construct a workflow

• How to add or remove different steps

• How to customize different parameters

• How to execute the workflow

• (Optional) How to install the workflow

Influenza Virus Typing and Variant Detection Using QIAGEN CLC Genomics Workbench

Tue, 16 Sep 2025 16:08:34 GMT

Join us for a focused webinar showcasing the Type Influenza Strain workflow within QIAGEN CLC Genomics Workbench. This streamlined, template-based workflow enables efficient typing of targeted Influenza virus sequencing data by integrating consensus sequence refinement, reference-based subtype identification and mixed-infection variant detection.

We’ll show how the workflow:

Automatically determines Influenza virus type and subtype
Outputs annotated consensus sequences with gene and CDS tracks for intuitive visualization
Detects low-frequency variants that may indicate mixed infections
Presents results in a consolidated, interactive track list in both nucleotide and amino acid views

Whether you’re tracking circulating strains or monitoring for emerging variants, this workflow offers a rapid and insightful approach to Influenza virus analysis.

Gene Fusion Detection Using QIAGEN CLC Genomics Workbench

Mon, 15 Sep 2025 09:58:21 GMT

This webinar will focus on running the fusion detection analysis within QIAGEN CLC Genomics Workbench and annotating the detected fusions using curated clinical knowledge from Human Somatic Mutation Database (HSMD). Finally, the data will be uploaded to QIAGEN Clinical Insight (QCI) applications for further analysis.

You will learn:

• How fusion detection algorithms work

• To run the fusion detection template workflow

• To interpret the analysis results

• To annotate fusions with HSMD

• To upload and analyze the fusions with QCI Interpret

HPV integration site mapping using QIAGEN CLC Genomics Workbench

Fri, 29 Aug 2025 09:21:10 GMT

Join us for an in-depth walkthrough of HPV integration site mapping using the CLC Microbial Genomics Module. This webinar presents a rapid, automated workflow for identifying and visualizing viral integration sites (VIS) in the human genome, using data from HPV-positive cervical samples. By leveraging the Viral Hybrid Capture (VHC) and VIS Identification workflows, researchers can perform end-to-end analysis—from taxonomic profiling to pinpointing virus-host breakpoints. Learn how this streamlined pipeline enables high-resolution visualization, accurate integration mapping, and efficient reporting to advance our understanding of HPV-driven carcinogenesis.

Key Takeaways:

• End-to-End Automation: Explore how the CLC Genomics Workbench streamlines HPV integration analysis using the VHC and VIS workflows.

• Rapid Analysis: Achieve full sample processing in under 25 minutes with minimal manual input.

• Integrated Visualization Tools: Leverage auto-generated circular plots and genomic breakpoints for clear interpretation of virus-host interactions.

• Reference-Driven Accuracy: Built-in HPV and human genome references enhance precision and reduce runtime.

• Clinical Impact: Identify disrupted and neighboring host genes that may serve as biomarkers or therapeutic targets.

• Accessible & Scalable: Designed for non-programmers, the GUI-based platform supports diverse sample types and study sizes.

The Forefront of Genomics Eric Green on Making Genomic Medicine a Reality

Wed, 20 Aug 2025 15:59:38 GMT

Since the completion of the Human Genome Project over two decades ago, genomics has become progressively entrenched within the bedrock of the biomedical research enterprise. Capitalizing on the momentum of the project’s successful completion, the field of genomics has increasingly expanded and matured, such that genomics is now central and catalytic in basic and translational research, and studies now regularly demonstrate the vital role that genomic information can play in clinical care.

Looking ahead, the anticipated advances in technologies, biological insights, and clinical applications (among others) will lead to more widespread dissemination of genomics throughout biomedical research, a growing adoption of genomics into medical and public-health practices, and an increasing relevance of genomics in everyday life.

In this webinar, Eric Green, former director of the National Human Genome Research Institute at NIH, will discuss how the institute capitalizes on these opportunities by developing and leading initiatives that address the most pressing challenges at the forefront of genomics, with a particular emphasis on understanding the biological complexities of the human genome, on untangling the complex roles that genomic variants play in health and disease, and making genomics broadly and equitably integrated into medicine.

Speaker: Eric Green, MD, PhD

Former Director, National Human Genome Research Institute, National Institutes of Health

Eric Green is the former director of the National Human Genome Research Institute (NHGRI) at the National Institutes of Health (NIH). He was the third NHGRI director, having been appointed by NIH director Francis Collins in 2009.

Green was at NHGRI for more than 30 years, during which he held multiple key leadership roles prior to becoming the director. He served as the Institute’s scientific director for seven years, chief of the Genome Technology Branch for 13 years, and founding director of the NIH Intramural Sequencing Center for 12 years.

For just over two decades, Green directed an independent research program that included integral start-to-finish roles in the Human Genome Project and groundbreaking work on mapping, sequencing, and characterizing mammalian genomes.

Green earned his medical degree and doctorate in 1987 from Washington University in St. Louis — coincidentally, the word “genomics” was coined in that same year. Throughout his career, he has authored and co-authored more than 395 scientific publications. Green has earned multiple honors and awards, including election to the National Academy of Medicine in 2023.

Shared Pathways, Many Origins: How Diverse Genetic Risk Targets Share...

Wed, 20 Aug 2025 15:57:37 GMT

Over two decades of research have uncovered over 100 genes with rare mutations linked to autism spectrum disorder (ASD), yet transcriptomic and epigenetic analyses reveal convergent dysregulation patterns in ASD brain tissue. In this webinar, learn how Dr. Dan Geschwind and his team at UCLA combine bioinformatics and experimental approaches to show that both common and rare genetic variations converge during early fetal cortical development. Using the largest hiPSC patient cohort and cortical organoid models, they identified shared transcriptional changes and created a resource of isogenic lines with over 100 ASD-associated mutations. Their integrative, network-based approach aims to clarify how genetic risk influences neurodevelopment through transcriptional regulation.

Speaker: Dan Geschwind, MD, PhD

Gordon and Virginia MacDonald Distinguished Professor of Neurology, Psychiatry and Human Genetics

Senior Associate Dean and Associate Vice Chancellor of Precision Health, Institute for Precision Health (IPH)

University of California Los Angeles (UCLA)

RNA-seq data analysis using QIAGEN CLC Genomics Workbench

Tue, 12 Aug 2025 16:52:27 GMT

For your RNA-seq data, you will learn how to:

• Import FASTQ files, cell matrix files and metadata

• Download and/or import reference and annotations files

• Map reads to a reference genome

• Generate gene and transcript counts

• QC reports displaying % mapped reads etc.

• Generate visualizations of results, such as heatmaps, differential expression tables, PCA/PCOA plots, Venn diagrams, Sankey plot and more

• Easily customize RNA-seq workflows

• Export publication-quality graphics, tables and reports

Per audience request

• Send differential expression tables to QIAGEN Ingenuity Pathway Analysis directly from QIAGEN CLC Genomics Workbench to analyze and interpret relevant pathways

ChIP-seq, Histone-seq and Methyl-seq analysis using CLC Genomics Workbench

Thu, 26 Jun 2025 22:42:47 GMT

This training will focus on how a user can analyze their epigenomics data using QIAGEN CLC Genomics Workbench.

Specifically, the trainer will cover how to

• Import the raw sequencing data

• Download or import reference, metadata and other needed files

• Mapping reads to a reference genome

• Calling and visualizing peaks

• Export graphical and tabular results

In addition, per registrant feedback and the trainer discretion additional topics such as customizing the workflow, how to send data to Ingenuity Pathway Analysis and more may be covered.

De novo assembly, BLAST and genome finishing using CLC Genomics Workbench

Wed, 18 Jun 2025 15:20:48 GMT

This webinar will introduce users to the tools available for short reads (Illumina) as well as long reads (Oxford Nanopore, Pac Bio) de novo assembly in CLC Genomics Workbench. It will also go over other useful functionalities such as BLAST and genome finishing.

Participants will learn the following:

o Download and install needed plugins.

o Import data required for the analysis.

o Run the de novo assembly workflow.

o For long reads, improve a de novo assembly by polishing with short, high-quality reads.

o Map reads to a reference and visualize an assembly.

o For long reads, correct raw long reads for further analysis.

o Use BLAST to investigate the contigs.

o Analyze and assemble contigs through Genome Finishing tools.

RNA-seq analysis for long reads

Tue, 10 Jun 2025 16:43:30 GMT

This training will focus on how a user can analyze their long reads data using QIAGEN CLC Genomics Workbench.

Specifically, the trainer will cover how to

• Import the long reads data

• Download or import reference, metadata and other needed files

• Process such data and generate downstream RNA-seq outputs

• Export high resolution graphics and tables

In addition, per registrant feedback and trainer discretion additional topics such as customizing the workflow, how to send data to Ingenuity Pathway Analysis, Sankey plot and more may be covered.

Shotgun metagenomics taxonomic profiling using QIAGEN CLC Genomics Workbench

Tue, 03 Jun 2025 15:22:01 GMT

The QIAGEN CLC Microbial Genomics Module provides tools and workflows for many bioinformatics applications, including microbiome analysis, isolate characterization, functional metagenomics and antimicrobial resistance characterization. The module supports the analysis of bacterial, viral and eukaryotic (fungal) genomes and metagenomes.

This training focuses on whole shotgun metagenomics taxonomic profiling. Specifically, we’ll cover:

• An overview of the different tools within QIAGEN CLC Microbial Genomics Module and the research areas supported

• Taxonomic profiling

• Importing data

• Utilization of metadata

• Downloading and managing references

• Taxonomic profiling workflow (analytical pipeline)

• Downstream processing of abundance tables

• Creating and exporting high-quality graphics

Multimodal panels analysis using QIAGEN CLC Genomics Workbench

Thu, 15 May 2025 10:53:39 GMT

This training will go over how QIAGEN CLC Genomics Workbench can be used to analyze Multimodal Panels data.

Trainer will cover

• How to import your data and metadata and download reference and other needed files

• How to use workflow and customize it

• How to visualize and export the results

DNA-seq (whole genome, whole exome, DNA-panel) analyses using QIAGEN CLC...

Thu, 24 Apr 2025 15:29:42 GMT

In this training, we’ll go over how to easily perform DNA-seq (specifically whole genome, whole exome, DNA-panel and similar) analyses easily and effectively using QIAGEN CLC Genomics Workbench.

Together, we’ll explore:

• Read mapping

• Variant calling (SNPs, mutations, Indels and more)

• Annotations and filters

• Genome browser view

Please bring any questions you may have, and we will answer them during this training.

Isolate Typing, Strain Identification and Antimicrobial Resistance Analyses...

Tue, 22 Apr 2025 08:00:36 GMT

QIAGEN CLC Genomics Workbench provides tools and workflows for a broad range of bioinformatics applications, including microbiome analysis, isolate characterization through SNP and K-mer trees using NGS data, and antimicrobial resistance characterization. CLC Genomics Workbench is widely used for analyses of bacterial, viral and eukaryotic (fungal) genomes and metagenomes.

Topics covered in this webinar include:

I. Overview of different tools within MGM application and research areas supported

II. II. Focused review of isolate typing and characterization

III. a. How to import data

IV. b. Using metadata

V. c. Downloading and managing references, including databases of isolates/resistances/MLST

VI. d. Walkthrough of the "Type a Known Species" workflow and review of details for each isolate

VII. e. Creating SNP profiles to specific reference

VIII. f. Generate a SNP tree for isolate comparison

IX. g. Export tabular and high-quality graphical outputs in wide range of file formats

Workflow construction and customization using QIAGEN CLC Genomics Workbench

Wed, 16 Apr 2025 01:54:25 GMT

Recently we have received some requests from CLC users (as well as CLC RNA-seq certification participants) to go over workflow construction and customization using CLC Genomics Workbench. Accordingly, we are hosting this training. The term workflow refers to bioinformatics secondary analysis pipelines such as DNA-seq, RNA-seq, OTU clustering, de novo assembly and more offered by CLC Genomics Workbench.

In this training, the trainer will go over

• The basics of workflow construction

• How to visualize different steps of the workflow and customize different settings

• How to edit workflows (add/remove steps, lock/unlock parameters and more)

• How to share workflows

• How to install workflows

• Other workflow related topics

Overlaying Expression Data onto UMAP Plots using the Single Cell Analysis...

Thu, 03 Apr 2025 12:50:28 GMT

In this video, we show how to color cells based on the expression of genes of interest in a UMAP. We also demonstrate how to examine expression values from the plot in a selected group of cells.

Recent training webinar and tutorial that includes UMAP plot generation from single-cell data:

Single-cell RNA-seq, cell hashing and spatial transcriptomics

Tutorial: Perform Single-Cell RNA Expression and Velocity Analysis

Finding the Perfect CLC Tool for your Workflow

Thu, 03 Apr 2025 12:49:05 GMT

Here are some quick tips on locating tools in CLC Genomics Workbench version 25+

Visualizing Spatial Transcriptomics Data in CLC Genomics Workbench

Thu, 03 Apr 2025 12:47:47 GMT

How to import and visualize spatial transcriptomics data in CLC

Installing CLC Network License manager and Downloading Network Licenses on...

Thu, 03 Apr 2025 12:46:31 GMT

How to install the CLC network license manager, network licenses, and CLC Genomics Workbench on Windows

Convenient Way To Launch Analysis Tools from UMAP Plots in the Single Cell...

Thu, 03 Apr 2025 12:45:27 GMT

In this video, we demonstrate the different tools that can be launched directly from the UMAP plot with a simple right-click.

Recent training webinar and tutorial that includes UMAP plot generation from single-cell data:

Single-cell RNA-seq, cell hashing and spatial transcriptomics

Tutorial: Perform Single-Cell RNA Expression and Velocity Analysis

Importing Single Cell Data into CLC Genomics Workbench

Thu, 03 Apr 2025 12:44:12 GMT

Single cell expression matrices can be imported into CLC manually using the import single cell matrix tool or they can be imported automatically using workflows. https://resources.qiagenbioinformatics.com/manuals/clcsinglecellanalysis/current/index.php?manual=Import_Expression_Matrix.html

Precise Workflow Path Control using Branching Elements

Thu, 03 Apr 2025 12:42:35 GMT

Direct outputs through a workflow based on sequence count, coverage, and sample quality using branching elements https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Branching_elements.html

Wrapping external applications into QIAGEN CLC Genomics Workbench

Thu, 27 Mar 2025 09:48:58 GMT

QIAGEN’s CLC bioinformatics software portfolio provides user-friendly and intuitive solutions that run on any platform. This helps scientists to focus on the biology of their research without requiring them to write code, or compile and run software from the command line.

At QIAGEN we understand, however, that no single piece of software can meet the needs of every bioinformatics challenge. Sometimes, you need to supplement standard pipelines with your own scripts, open-source tools or third party applications from the command-line.

Accordingly, this training will go over:

• A quick introduction to CLC Genomics Workbench

• Wrapping an external application into the CLC environment

• Running external application alongside CLC tools and exporting results.

RNA-seq data analysis using QIAGEN CLC Genomics Workbench

Tue, 25 Mar 2025 12:35:35 GMT

For RNA-seq data, you will learn how to:

• Import FASTQ files, cell matrix files and metadata and how to download references

• Map reads to a reference genome and generate gene and transcript counts and QC reports displaying % mapped reads, knee plots, etc.

• Generate visualizations of results, such as heatmaps, differential expression tables, PCA/PCOA plots, Venn diagrams, sankey plot and others

• Easily customize RNA-seq workflows • Export publication-quality graphics, tables and reports

Per audience request

• Send differential expression tables to QIAGEN Ingenuity Pathway Analysis directly from QIAGEN CLC Genomics Workbench to analyze and interpret relevant pathways

Analysis of microbial communities for biotransformation, biodegradation and...

Tue, 25 Mar 2025 11:01:07 GMT

Geomicrobiology and petroleum microbiology are important fields that study how microbes interact with geological, geochemical, and petroleum processes. Understanding the composition of microbial communities can advance our knowledge of biotransformation, biodegradation, and bioremediation in industries such as environmental engineering, mining, and oil and gas.

QIAGEN CLC Genomics Workbench and the Microbial Genomics Module provide tools and workflows for a broad range of bioinformatics applications, including microbiome analysis, isolate characterization, and functional metagenomics. This webinar will focus on amplicon-based taxonomic profiling (16S/18S/ITS sequencing OTU clustering) using data collected from oil reservoirs. Specifically, the trainer will be:

• Highlighting different tools within the MGM application and research areas supported

• For taxonomic profiling:

o Importing data

o Utilizing metadata

o Downloading and managing references

o Launching the OTU clustering workflow (analytical pipeline)

• Downstream processing of abundance tables

• Creating and exporting high-quality graphics

Long reads analysis with QIAGEN CLC Genomics Workbench

Tue, 25 Feb 2025 20:59:02 GMT

Workflow construction and customization using QIAGEN CLC Genomics Workbench

Thu, 13 Feb 2025 16:06:53 GMT

In this training, the trainer will go over

• The basics of workflow construction

• How to visualize different steps of the workflow and customize different settings

• How to edit workflows (add/remove steps, lock/unlock parameters and more)

• How to share workflows

• How to install workflows

• Other workflow related topics

What's new in QIAGEN CLC Genomics version 25

Sun, 26 Jan 2025 23:17:36 GMT

Single - cell RNA-seq, cell hashing and spatial transcriptomics

Thu, 23 Jan 2025 13:42:27 GMT

In this training, you will learn how to analyze and interpret your own single cell RNA-seq data using QIAGEN CLC Genomics Workbench starting with either FASTQ or matrix files.

Using CLC Genomics Workbench, you will learn how to perform secondary analysis on your single cell RNA-seq data. Specifically, you will learn how to:

• Import your raw FASTQ or processed cell-matrix files.

• Use pre-configured but customizable pipelines/workflows for single cell RNA-seq data.

• Generate high resolution visuals and other files from your analysis for publications and biopharmaceutical discoveries.

o Dimension reduction (UMAP, t-SNE) plots

o Differential expression table for clusters, cell types, or combination of both

o Heat map

o Dot plots

o Violin plots

• Learn how to use “Create Cell Annotations from Hashtags” for cell hashing (i.e., CITE-seq).

• Dive into spatial transcriptomic analysis, the latest feature in the single cell RNA-seq module.

Sanger sequencing, alignment, cloning, primer design and more using QIAGEN...

Thu, 23 Jan 2025 12:52:40 GMT

This training will be relevant to both QIAGEN Main and Genomics workbench users and prospects who are interested in below analytics.

• Alignment and tree construction

• Sanger sequencing analysis

• Cloning and primer design

• Other molecular biology tools

Get started with QIAGEN CLC Genomics Workbench

Mon, 16 Dec 2024 09:47:47 GMT

Start out strong with QIAGEN CLC Genomics Workbench and follow along with our live demo of its popular features.

We’ll cover how to:

Install and set up your Workbench

Add plugins like Biomedical Genomics Analysis plugin

Manage data with Reference Data Management

Work with reads and using tools and workflows to batch process your data

Visualize data with Track List and Genome Browser

Export data and share workflows

If you have any questions, we’ll answer them during the webinar.

Detecting copy number variants with QIAGEN CLC Genomics Workbench

Tue, 10 Dec 2024 00:32:37 GMT

Learn how to use the copy number variant (CNV) detection tool in the QIAGEN CLC Genomics Workbench to examine your exome and targeted resequencing data.

Our live demo will cover:

• Using the CNV detection algorithm for exome and targeted resequencing data

• Adding the CNV detection tool to workflows

• Visualizing your results

Investigating genomic variants using QIAGEN CLC Genomics Workbench, QCI...

Thu, 21 Nov 2024 10:48:34 GMT

In this webinar, attendees will have the opportunity to:

1. Learn how to import whole genome or exome sequencing data into QIAGEN CLC Genomics Workbench and use the ultra-fast LightSpeed Module that delivers end-to-end NGS FASTQ to VCF pipeline;

2. Explore capabilities in QCII-T which can enable scientists to accelerate discoveries from hereditary or tumor cohort analyses to find associations between gene variants and diseases;

3. Learn how to use IPA and its manually curated content among other integrated scientific evidence to uncover novel biological mechanisms underlying these gene variants.

How to install plugins in a CLC Workbench?

Wed, 20 Nov 2024 11:55:40 GMT

Long reads analysis with QIAGEN CLC Genomics Workbench

Fri, 25 Oct 2024 12:43:16 GMT

This webinar will introduce users to the long read support plugin for Oxford Nanopore and PacBio sequencing reads in QIAGEN CLC Genomics Workbench.

Participants will learn how to:

• Download and install needed plugins

• Import data required for the analysis

• Perform long read de novo assembly

• Map reads to a reference and visualize an assembly

• Use BLAST to investigate the contigs

• Use additional long read tools: polish with short reads, structural variant calling

• Use genome finishing tools: analyze and assemble contigs

• Use analytical tools: RNA-seq analysis for long reads, classify long read amplicons for metagenomics

RNA-seq data analysis and interpretation with Sankey plot update

Tue, 08 Oct 2024 16:26:05 GMT

For RNA-seq data, you will learn how to:

• Import FASTQ files, cell matrix files and metadata and how to download references

• Map reads to a reference genome and generate gene and transcript counts and QC reports displaying % mapped reads, knee plots, etc.

• Generate visualizations of results, such as heatmaps, differential expression tables, PCA/PCOA plots, Venn diagrams, sankey plot and others

• Easily customize RNA-seq workflows

• Export publication-quality graphics, tables and reports

• Send differential expression tables to QIAGEN Ingenuity Pathway Analysis directly from QIAGEN CLC Genomics Workbench to analyze and interpret relevant pathways

Single-cell RNA-seq, cell hashing, and spatial transcriptomics

Mon, 26 Aug 2024 16:01:12 GMT

A slide illustrating some of the many result types/graphics you will be able to generate after this training. https://qiagen.showpad.com/share/jYTCDPNfz1SdIMPQPSPYS

Analyze and interpret your own single-cell RNA-seq data using QIAGEN CLC Genomics Workbench, starting with either FASTQ or matrix files.

Learn how to perform the different steps of secondary analysis on your single-cell RNA-seq data, such as:

• Importing your raw FASTQ or processed cell-matrix files
• Using preconfigured but customizable pipelines/workflows for single-cell RNA-seq data.
• Generating high-resolution visuals and other files from your analysis, for publications and biopharmaceutical discoveries.
o Dimension reduction (UMAP, t-SNE) plots
o Differential expression tables for clusters, cell types or a combination of both
o Heat maps o Dot plots o Violin plots
• Using the “Create Cell Annotations from Hashtags” tool for cell hashing (e.g., CITE-seq).
• Applying spatial transcriptomic analysis, the latest feature in the single-cell RNA-seq module

Antimicrobial resistance (AMR) and multi-locus sequence typing (MLST) with...

Mon, 22 Jul 2024 15:37:11 GMT

You asked, and we’re here to deliver. In this training, we’ll cover how antimicrobial resistance (AMR) is used for isolation or can be easily integrated with other functionalities such as multi-locus sequence typing (MLST).

In this training, we’ll cover:
• Introduction to AMR, MLST and relevant databases
• QIAGEN Microbial Insight - Antimicrobial Resistance database (QMI-AR)
• Importing data and downloading needed databases
• Finding resistance with nucleotide DB, PointFinder and ShortBRED
• Integrating AMR with MLST
• Exporting high-resolution graphics and result tables.

De novo assembly, BLAST and genome finishing with QIAGEN CLC Genomics Workbench

Thu, 18 Jul 2024 18:31:45 GMT

Participants will learn the following:
o Download and install needed plugins.
o Import data required for the analysis.
o Run the de novo assembly workflow.
o For long reads, improve a de novo assembly by polishing with short, high-quality reads.
o Map reads to a reference and visualize an assembly.
o For long reads, correct raw long reads for further analysis.
o Use BLAST to investigate the contigs.
o Analyze and assemble contigs through Genome Finishing tools.

Streamline H5N1 and other microbial samples with CLC Genomics Workbench

Thu, 23 May 2024 15:17:00 GMT

In this training, you will learn how to analyze viral samples using QIAGEN CLC Genomics Workbench. This webinar will focus on bioinformatics workflows and data interpretation using H5N1 as an example, but similar analysis can be done with other viral and microbial (bacteria, fungus and more) samples.

Using viral samples, you will learn how to:

• Utilize molecular biology tools such as primer design, cloning, alignment and tree construction and Sanger sequencing analysis
• Profile the virus present in a sample and automatically generate read mappings, detect variants, annotate consensus sequences, BLAST annotated consensus sequence genes and build phylogenetic trees for top hits and their close relatives
• Microbial genomics analysis including OTU clustering, taxonomic profiling and functional analysis
• Additional topics of interest based on registration feedback

QIAGEN CLC Genomics Workbench is a user-friendly bioinformatics software solutions for genomics, transcriptomics, epigenomics and metagenomics analysis in one program.

Scale up NGS bioinformatics analysis throughput with CLC Genomics Server and...

Thu, 23 May 2024 14:00:26 GMT

More and more biopharma and academic groups are looking to process a large number of samples simultaneously or for a quicker turnaround time. This webinar will introduce a flexible and powerful setup for running your NGS sequence analyses through servers or Amazon Web Services (AWS), depending on user preference. We will demonstrate how CLC Genomics Workbench can be used to customize workflows and send analyses for batch execution. We will also highlight analysis automation solutions, use of third-party dockers, audit trails and user management – all of which are available with the CLC Genomics Server software.

You will learn to:
• Customize template workflows to meet your NGS analysis requirements
• Set up a CLC Genomics Cloud environment on AWS
• Submit workflows to run on internal servers or AWS and retrieve results from these analyses
• Use third-party dockers and automate workflow execution

DNA-seq analyses (whole genome, whole exome, panel) using QIAGEN CLC...

Thu, 02 May 2024 17:09:28 GMT

In this training, we’ll go over how to easily perform DNA-seq analyses (for whole genome, whole exome, panel and similar) easily and effectively using QIAGEN CLC Genomics Workbench.

Together, we’ll explore:

• Read mapping
• Variant calling (SNPs, mutations, Indels and more)
• Annotations and filters
• Genome Browser

Single Cell RNA-Seq, Cell Hashing, and Spatial Transcriptomics

Tue, 26 Mar 2024 14:46:00 GMT

In this training, you will learn how to analyze and interpret your own single cell RNA-seq data using QIAGEN CLC Genomics Workbench starting with either FASTQ or matrix files.

Using CLC Genomics Workbench, you will learn how to perform secondary analysis on your single cell RNA-seq data. Specifically, you will learn how to:
• Import your raw FASTQ or processed cell-matrix files.
• Use pre-configured but customizable pipelines/workflows for single cell RNA-seq data.
• Generate high resolution visuals and other files from your analysis for publications and biopharmaceutical discoveries.
o Dimension reduction (UMAP, t-SNE) plots
o Differential expression table for clusters, cell types, or combination of both
o Heat map
o Dot plots
o Violin plots
• Learn how to use “Create Cell Annotations from Hashtags” for cell hashing (i.e., CITE-seq).
• Dive into spatial transcriptomic analysis, the latest feature in the single cell RNA-seq module.

Workflow construction and customization using QIAGEN CLC Genomics Workbench

Thu, 22 Feb 2024 08:40:00 GMT

In this training, the trainer will go over
• The basics of workflow construction
• How to visualize different steps of the workflow and customize different settings
• How to edit workflows (add/remove steps, lock/unlock parameters and more)
• How to share workflows
• How to install workflows
• Other workflow related topics

Long reads analysis using QIAGEN CLC Genomics workbench (with new features -...

Tue, 13 Feb 2024 13:25:00 GMT

This webinar will introduce users to the long read support plugin for Oxford Nanopore and PacBio sequencing reads in QIAGEN CLC Genomics Workbench.

Participants will learn the following:

• Download and install needed plugins.
• Import data required for the analysis.
• Long read de novo assembly.
• Map reads to a reference and visualize an assembly.
• Use BLAST to investigate the contigs.
• Additional long read tools: polish with short reads, structural variant calling.
• Genome finishing tools: analyze and assemble contigs
• Analytical tools: RNA-seq analysis for long reads, classify long read amplicons for metagenomics.

What’s new in QIAGEN CLC Genomics Workbench version 24

Wed, 31 Jan 2024 14:19:21 GMT

QIAGEN CLC Genomics Workbench version 24 is here with exciting updates we'd like to share with you. These include:

Our QIAGEN CLC LightSpeed Module which now provides ultrafast somatic workflows
Spatial Transcriptomics and ParseBio support in QIAGEN CLC Single Cell Analysis Module
Amplicon classification for ONT reads in QIAGEN CLC Microbial Genomics Module
New Structural variant detection for long read and De novo assembly of PacBio HiFi reads
Importer for Element, PacBio Onso, Ultima reads, Singular
CRAM format importer / exporter
Fancy new interactive RNAseq Volcano plot for RNAseq
And many more new and improved workflow and reporting capabilities
Join this webinar to:

Learn how to take advantage of the latest improvements
Get an overview of the many tools available to you
Make sure to join this webinar to elevate your understanding of current trends in bioinformatics

Exploring RNA-seq data using the CLC Genomics Workbench: Expression Analysis...

Wed, 24 Jan 2024 13:17:00 GMT

In this webinar, we will present how to analyze RNA-seq data starting from raw sequencing reads. We will touch upon expression analysis, statistical comparison, visualization and functional enrichment of RNA-seq data using an actual dataset and a live demo.

During this webinar we will cover:
• Mapping of reads to the reference and abundance estimation
• Principal component analysis (PCA) of RNA-seq data
• Differential expression analysis
• Visualization of results using volcano plots, heatmaps and Venn diagrams
• Creating RNA-seq expression table and adding GO annotations
• Gene set enrichment analysis using hypergeometric test
• Ready-to-use Workflows for expression analysis
• Upload to Ingenuity Pathway Analysis (IPA)

Sanger sequencing, alignment, cloning, primer design and more using QIAGEN...

Wed, 17 Jan 2024 18:35:38 GMT

If you're a QIAGEN CLC Main and/or Genomics Workbench user, or interested in learning about the below analytics, you won't want to miss this training:

• Alignment and tree construction
• Sanger sequencing analysis
• Cloning and primer design
• Other molecular biology tools

RNA-seq data analysis and interpretation with Sankey plot update

Mon, 18 Dec 2023 12:12:03 GMT

During this 120-minute training, we’ll teach you how to easily analyze and interpret RNA-seq data using QIAGEN CLC Genomics Workbench and QIAGEN Ingenuity Pathway Analysis (IPA) software.

For RNA-seq data, you will learn how to:
• Import FASTQ files, cell-matrix files and metadata and how to download references
• Map reads to a reference genome and generate gene and transcript counts and QC reports displaying % mapped reads, knee plots, etc.
• Generate visualizations of results, such as heatmaps, differential expression tables, PCA/PCOA plots, Venn diagrams, sankey plot and others
• Easily customize RNA-seq workflows
• Export publication-quality graphics, tables and reports
• Send differential expression tables to QIAGEN Ingenuity Pathway Analysis directly from QIAGEN CLC Genomics Workbench to analyze and interpret relevant pathways

How to perform DNA-seq and resequencing data analyses using QIAGEN CLC...

Mon, 18 Dec 2023 12:07:03 GMT

In this webinar, we’ll introduce algorithms required to perform data analysis for resequencing next-generation sequencing data. Together, we’ll explore:

• Read mapper
• Variant callers
• Annotations and filters
• Genome Browser

QIAGEN CLC Genomics Workbench for your miRNA data analyses

Tue, 05 Dec 2023 14:10:47 GMT

Join us for our webinar, where we‘ll focus on miRNA data analysis using QIAGEN CLC Genomics Workbench and Biomedical Genomics Analysis plugin. Together, we‘ll explore how you can:
• Import reads and metadata
• Download miRBase database
• Quantify miRNA expression
• Perform differential expression analysis
• Visualize your results
• Create and use a custom database

Circulating Tumor Cell Detection and Analysis to Support Malignancy...

Wed, 25 Oct 2023 14:11:11 GMT

Circulating tumor cells (CTCs) are cells that leave the primary tumor and are intravasated into the blood circulation system. A subset of those make it to other organs and are responsible for metastasis. iCellate’s CellMate platform is a CTC-based liquid biopsy for cancer cell enrichment, detection, and biomarker analysis via a simple blood draw.

In this seminar, you’ll learn:

From Helena Silva Cascales, senior scientist at iCellate Medical AB, how the isolation of whole-tumor cells provides a more comprehensive biomarker analysis, including genomic sequencing and multiplexed protein expression analysis.
From Kashyap Dave, principal scientist at iCellate Medical AB, how DNA from single CTCs can be amplified, sequenced, and analyzed to support malignancy designation and tissue of origin identification using classification analyses under development within Qiagen CLC Genomics Workbench.

RNA-seq data analysis and interpretation using QIAGEN CLC and QIAGEN IPA

Wed, 18 Oct 2023 14:41:28 GMT

This 120-minute training will teach you how to easily analyze and interpret RNA-seq data using QIAGEN CLC Genomics Workbench software and QIAGEN Ingenuity Pathway Analysis (IPA).

For RNA-seq data, you will learn how to:
• Import FASTQ files, cell matrix files and metadata and how to download references
• Map reads to a reference genome and generate gene and transcript counts and QC reports displaying % mapped reads, knee plots, etc.
• Generate visualizations of results, such as heatmaps, differential expression tables, PCA/PCOA plots, Venn diagrams and others
• Easily customize RNA-seq workflows
• Export publication-quality graphics, tables and reports
• Send differential expression tables to QIAGEN Ingenuity Pathway Analysis directly from QIAGEN CLC Genomics Workbench to analyze and interpret relevant pathways

Scale up NGS bioinformatics analysis throughput with QIAGEN CLC Genomics...

Wed, 11 Oct 2023 14:28:41 GMT

Scale your NGS analysis to match your sequencing throughput using our QIAGEN CLC Genomics cloud solution. In this webinar, you’ll learn about the flexible and powerful setup for running your NGS sequence analyses on Amazon Web Services (AWS). You’ll learn how to use QIAGEN CLC Genomics Workbench to customize workflows and send analyses to AWS Batch for execution. Together we’ll also explore analysis automation solutions, third-party dockers, audit trails and user management, all of which are available with QIAGEN CLC Genomics Server software.

Together, we’ll explore how to:
• Customize template workflows to meet your NGS analysis requirements
• Set up a QIAGEN CLC Genomics cloud environment on AWS
• Submit workflows to run on AWS and to retrieve results from these analyses.
• Use third-party dockers and automate workflow execution

Analyzing QIAseq DNA Panels with QIAGEN CLC Genomics Workbench

Thu, 21 Sep 2023 15:55:27 GMT

This training will focus on analyzing QIAseq DNA panel datasets with QIAGEN CLC Genomics Workbench and the Biomedical Genomics Analysis plugin, including a live “FASTQ-to-VCF” demo of data import, data analysis and investigation. We will also show how to set up the analysis of a custom QIAseq DNA panel.

During this training, you’ll learn about:
• Import of FASTQ files
• Launching an analysis workflow
• Inspection of QC reports, genome browser view, detected variants and other workflow outputs
• Customization of template workflow parameters based on findings in the QC report
• Import of custom primers and target regions file
• How to set up an analysis of a custom panel

Metagenomics and taxonomic profiling using amplicon sequence variants (ASVs)

Thu, 14 Sep 2023 19:22:11 GMT

When it comes to taxonomic profiling of the microbiome, amplicon sequence variants (ASVs) is a method that has unique benefits compared to the traditional method of sequence similarity-based operational taxonomic unit (OTU) clustering. This training’ll cover how to effectively do taxonomic profiling using QIAGEN CLC Genomics Workbench’s ASV tools and a customizable workflow.

Specifically, you’ll learn how to:
1. Collect and bin sequence variants for each sample
2. Merge AVS tables to compare profiles
3. Assign the taxonomic profile/organism
4. Export high-resolution graphical and comprehensive tabular results

Part I: Single-cell RNA sequencing data analysis using QIAGEN CLC Genomics...

Mon, 21 Aug 2023 20:06:25 GMT

This two-part series will walk you through single-cell RNA sequencing (scRNA-seq) analysis starting with a matrix file or FASTQ files and ending with a deep understanding of key pathways, regulators and cell type signatures within your data.

This session is for part I of this training. In this session, you'll learn to use QIAGEN CLC Genomics Workbench to perform secondary analysis on your scRNA-seq data. Specifically, you will learn how to:
• Import your raw FASTQ or processed cell-matrix files
• Use pre-configured but customizable pipelines/workflows for scRNA-seq data
• Generate high-resolution visuals and other files from your analysis for publications and biopharmaceutical discoveries. These include:

o UMAP, t-SNE plots
o Differential expression table for clusters, cell types, or a combination of both
o Heat map
o Dot plots
o Violin plots

Part II of this training takes place on Wednesday, Aug. 16. It focuses on interpreting scRNA-seq data using QIAGEN Ingenuity Pathway Analysis (IPA) to understand key pathways, regulators and cell type signatures within your data. Click here to watch Part II: https://tv.qiagenbioinformatics.com/video/87882212/part-ii-single-cell-rna-sequencing

Immune repertoire analysis using QIAGEN CLC Genomics Workbench

Mon, 21 Aug 2023 15:57:03 GMT

The composition of the immune repertoire, consisting of the T cell and B cell receptors (TCR and BCR), is important for an organism's adaptive immune system and plays a pivotal role in an individual's overall health. Understanding the complex array of TCR and BCR allows for developing precision medicine and immunotherapy. Analyzing next-generation sequencing (NGS) data from RNA-seq experiments to characterize and understand TCR and BCR clonotypes may aid in identifying cases that could benefit from personalized immunotherapy or potentially predict therapeutic outcomes.

In this training, we'll use QIAGEN CLC Genomics Workbench to analyze immune repertoire NGS data generated from RNA-seq or single-cell RNA-seq data. Together we'll explore how to import, analyze and interpret your NGS data. Specifically, you'll learn how to:

-Import NGS data into QIAGEN CLC Genomics Workbench

-Analyze the data using template workflows

-Interpret the results using the interactive graphics produced by the workflows

Metagenomics taxonomic profiling using QIAGEN CLC Genomics Workbench

Fri, 28 Jul 2023 16:44:53 GMT

QIAGEN CLC Microbial Genomics Module provides tools and workflows for many various bioinformatics applications, including microbiome analysis, isolate characterization, functional metagenomics and antimicrobial resistance characterization. The module supports the analysis of bacterial, viral and eukaryotic (fungal) genomes and metagenomes.

This training focuses on amplicon-based taxonomic profiling (16S/18S/ITS sequencing OTU clustering). Specifically, we’ll cover together:

• An overview of the different tools within QIAGEN CLC Microbial Genomics Module and the research areas supported

• Taxonomic profiling

• Importing data

• Utilization of metadata

• Downloading and managing references

• The OTU clustering workflow (analytical pipeline)

• Downstream processing of abundance tables

• Creating and exporting high-quality graphics

Investigating genomic variants using QIAGEN CLC Genomics Workbench, QCI...

Fri, 21 Jul 2023 15:27:54 GMT

Discovering new genes implicated in hereditary diseases or cancer progression is challenging yet advancing rapidly due to the increase in next-generation sequencing (NGS) cohort data. These data analyses produce insights into associations between gene variants and diseases and the biological mechanisms of these gene variants.

By combining QIAGEN CLC Genomics Workbench, QCII-T and QIAGEN IPA, you can analyze sequencing data obtained from a variety of NGS technologies, annotate gene variants using the world’s most comprehensive and up-to-date curated scientific evidence and find biological connections in gene variants with manually curated scientific findings. Using a streamlined NGS analysis workflow, you’ll get valuable and reliable insights for your research project and speed up your discoveries.

In this training, you’ll:
1. Learn to import whole genome or exosome sequencing data into QIAGEN CLC Genomics Workbench and use the ultra-fast LightSpeed Module that delivers an end-to-end NGS FASTQ to VCF pipeline
2. Explore the capabilities in QCII-T which can help accelerate your discoveries from hereditary or tumor cohort analyses to find associations between gene variants and diseases
3. Learn how to use QIAGEN IPA and its manually curated content, among other integrated scientific evidence, to uncover novel biological mechanisms underlying these gene variants

Pathogen detection and variant analysis using hybrid capture technology and...

Fri, 21 Jul 2023 14:59:07 GMT

The detection and surveillance of pathogens such as respiratory viruses, sexually transmitted pathogens, adventitious agents and antimicrobial-resistant bacteria are increasingly important in healthcare settings and environmental monitoring. The COVID-19 pandemic highlighted the importance of identifying and differentiating variants of concern. By applying the lessons learned from the COVID-19 pandemic to other pathogens of interest, it’s clear there’s a widespread need for the ability to target sensitive variants using next-generation sequencing (NGS) enrichment strategies and to analyze NGS data.

In this training, we'll use QIAGEN CLC Genomics Workbench to analyze NGS data generated from hybrid capture technology. Using data generated from QIAGEN HYB panels, you'll learn how to import, analyze and interpret NGS data. Specifically, you’ll discover:
1. How to import NGS data into QIAGEN CLC Genomics Workbench
2. How to analyze the data using template workflows;
3. How to interpret the results using the interactive graphics produced by the workflows;
4. How to modify the template workflows to accommodate custom panels

De novo assembly, BLAST and genome finishing using QIAGEN CLC Genomics Workbench

Tue, 27 Jun 2023 15:39:00 GMT

Participants will learn the following:

o Download and install needed plugins.

o Import data required for the analysis.

o Run the de novo assembly workflow.

o For long reads, improve a de novo assembly by polishing with short, high-quality reads.

o Map reads to a reference and visualize an assembly.

o For long reads, correct raw long reads for further analysis.

o Use BLAST to investigate the contigs.

o Analyze and assemble contigs through Genome Finishing tools.

Antimicrobial resistance (AMR) and multi-locus sequence typing (MLST) using...

Thu, 08 Jun 2023 18:33:00 GMT

You asked for it by popular demand, and we’re here to deliver. In this training, we’ll cover how antimicrobial resistance (AMR) is used for isolation or can be easily integrated with other functionalities such as multi-locus sequence typing (MLST).
In this training, we’ll cover:
• Introduction to AMR, MLST and relevant databases
• QIAGEN Microbial Insight - Antimicrobial Resistance database (QMI-AR)
• Importing data and downloading needed databases
• Finding resistance with nucleotide DB, PointFinder and ShortBRED
• Integrating AMR with MLST
• Exporting high-resolution graphics and result tables

Beyond exomes: Ultrafast FASTQ to interpretation

Tue, 09 May 2023 20:00:00 GMT

QIAGEN CLC LightSpeed Module delivers an ultra-fast, end-to-end hereditary NGS FASTQ to VCF pipeline. LightSpeed takes raw FASTQ files generated by paired-end 150 bp sequencing protocols and performs quality trimming, adapter trimming, read mapping, deduplication, local realignment, QC and germline variant calling.

QIAGEN CLC Genomics Cloud computing software allows you to launch analyses from CLC Workbenches or CLC Servers for execution on Amazon Web Services (AWS).

For more details, visit https://digitalinsights.qiagen.com/explore/c/qpro-2367_an_clc-lig?x=QbXlDs#page=1 and
https://digitalinsights.qiagen.com/plugins/clc-cloud-module/

To start a trial of QIAGEN CLC Genomics Workbench Premium, visit:
https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-clc-workbench-premium/

In this training, we’ll explore together:

• An overview of the QIAGEN CLC Genomics Workbench Premium platform
• An overview of the QIAGEN CLC Genomics Server and Cloud • Breaking the speed of light
• Why LightSpeed is arguably the fastest and cheapest-to-run hereditary FASTQ-to-VCF WGS pipeline available
• Benchmarks/comparisons
• Demo of lightspeed and cloud module for Fastq to VCF
• Plugin installation
• Download of reference(s)
• Workflow execution and results review

Pathogen detection in wastewater samples using QIAGEN CLC Genomics Workbench

Mon, 24 Apr 2023 18:22:10 GMT

In this 90-minute training, you will learn how to easily analyze wastewater samples to detect pathogens (SARS-COV2, etc.) using QIAGEN CLC Genomics Workbench software.

You will learn how to:
• Importing reads
• Open and modify prebuilt workflow (analysis pipeline)
• Install and execute workflow
• Review QC reports
• Perform genome visualization
• Export the consensus sequence in FASTA format to upload to Pangolin
• Create a SNP tree of the consensus sequence and overlay Pangolin information
• Export graphical and tabular results

QIAGEN Bioinformatics Public Health Summit

Fri, 31 Mar 2023 17:16:26 GMT

As next-generation sequencing (NGS) technologies become more available, public health labs face increasing pressure to use them to identify and characterize infectious diseases, microbial pathogens and outbreaks. However, each task may require specific data processing and analysis methods, making NGS seem daunting.

Our Public Health Lab NGS Summit is a virtual event focusing on applying NGS data analysis in your public health laboratory. We'll cover the basics of NGS data analysis, workflow selection, and expected outputs for outbreak investigations, disease surveillance and antimicrobial resistance. We'll also highlight a panel of peers with real-world experience in NGS data analysis in public health.

Topics of interest:
• Enteric pathogens
• Pathogens of concern – Vector-borne diseases, TB, sexually transmitted infections
• Respiratory viruses – SARS-CoV-2, influenza, RSV
• Wastewater applications
• Services for extending internal resources
• License options for QIAGEN products
• Round table discussion from public health experts using NGS

Lowering NGS analysis cost at lightspeed

Wed, 29 Mar 2023 14:55:48 GMT

Advances in next-generation sequencing (NGS) technologies over the years have significantly decreased the cost of whole genome (WGS) and whole exome (WES) applications, such that they are considered the standard of care within multiple healthcare organizations. Arguably, the most significant NGS challenges lie within data analysis and interpretation. Various parameters such as sensitivity, specificity, cost and speed are critical for secondary analysis, while accurate, comprehensive and up-to-date content is required for reliable interpretation. These aspects are crucial, especially where rapid turnaround times are critical for improved health outcomes. There is no better example than the implementation of WES and WGS in the neonatal and pediatric intensive care units (NICU/PICU).

Watch this webinar to learn about QIAGEN CLC LightSpeed, a secondary analysis software that dramatically reduces the cost and time it takes to analyze WES and WGS data and generate actionable insights.

Key learning objectives

Learn how to process FASTQ files to obtain quality variant calls in minutes
Discover how LightSpeed can be used on existing laptops, desktops, servers, HPC or in the cloud
Learn how LightSpeed will reduce your cost without sacrificing quality
Explore how LightSpeed enables the fastest WES and WGS workflow from FASTQ to report

What’s new in QIAGEN CLC Genomics Workbench version 23

Fri, 03 Feb 2023 04:39:22 GMT

QIAGEN CLC Genomics Workbench version 23 is here with exciting updates we'd like to share with you. These include:

Our new QIAGEN CLC LightSpeed Module which provides the world’s fastest and cheapest whole genome sequencing (WGS) and (WES) analyses
Our new and improved QIAGEN CLC Cloud Module which provides direct access to your AWS S3 files and frees up your local workbench resources
New capabilities in QIAGEN CLC Microbial Genomics Module
New analyses in QIAGEN CLC Single Cell Analysis Module
New cloning tools
And many more new and improved workflow capabilities

16S/18S/ITS sequencing analysis using CLC Genomics Workbench

Wed, 25 Jan 2023 17:30:08 GMT

This training will be focused on amplicon-based taxonomic profiling (16S/18S/ITS sequencing OTU clustering). The trainer will cover:

· Overview of different tools within QIAGEN CLC Microbial Genomics Module and research areas supported

· For taxonomic profiling

o Importing data

o Utilization of metadata

o Downloading and managing references

o Walk through of OTU clustering workflow (analytical pipeline)

o Downstream processing of abundance tables

o Creating and exporting high-quality graphics

Understanding and maximising QIAseq secondary analysis in the QIAGEN CLC...

Fri, 04 Nov 2022 13:50:26 GMT

Join us for a 60 minute training session where attendees will understand how to analyse data from targeted DNA and RNAscan panels using the QIAGEN CLC Genomics Workbench and how to adapt existing workflows to best suit laboratory-specific requirements.

RNA-seq and single-cell RNA-seq data analysis

Mon, 09 May 2022 16:24:58 GMT

In this 90-minute training, users will learn how to easily analyze RNA-seq and single-cell RNA-seq (scRNA-seq) data using QIAGEN CLC Genomics Workbench software.

For RNA-seq and scRNA-seq data, users will learn how to:
• Import fastq files, cell matrix files and metadata and how to download references
• Map reads to a reference genome and generate gene and transcript counts and QC reports displaying % mapped reads, knee plots, etc.
• Generate visualizations of results, such as heatmaps, differential expression tables, PCA/PCOA plots, t-SNE plots, UMAP plots, dot plots, Venn diagrams and others
• Annotate single-cell clusters overlain with gene expression
• Easily customize RNA-seq and scRNA-seq workflows
• Export publication-quality graphics, tables and reports
• Send differential expression table to QIAGEN Ingenuity Pathway Analysis directly from QIAGEN CLC Genomics Workbench

Single Cell ATAC sequence analysis

Mon, 25 Apr 2022 16:15:11 GMT

scATAC-seq (Single-Cell Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to assess chromatin accessibility. Now with QIAGEN CLC Genomics Workbench Premium, we put the power of this growing technology at your fingertips.

In this webinar training, our QIAGEN Field Application Scientist will walk you through a typical scATAC-seq workflow. Topics covered will include:
• Read QC and deduplication
• Peak calling
• Finding nearby genes and transcription factor (TF) motif scans
• Automatically prediction of cell types and cluster
• Comprehensive QC report
• Various other visualization, such as UMAP plot, Dot plots, heat map, and Violin Plots

Long-read sequencing analysis in the QIAGEN CLC Genomics Workbench

Thu, 24 Mar 2022 07:45:16 GMT

This tutorial is an introduction to working with the tools in the Long Read Support (beta) plugin. The Long Read Support (beta) plugin is a collection of tools developed for working with long, error-prone reads such as those produced by the single-molecule sequencing technologies of Pacific Biosciences or Oxford Nanopore Technologies.

Participants will take away how to:

• Download Plugin for Long read support
• Import data required for the analysis
• De novo assembly of a microbial sized genome using long, error-prone reads
• Improve a de novo assembly from long reads by polishing with short, high-quality reads
• Map long reads to a reference and visualizing an assembly
• Correct raw long reads for further analysis