tv.qiagenbioinformatics.com

QIAGEN CLC Genomics Workbench 20 – scalable desktop software for NGS data...

Thu, 10 Jul 2025 15:51:32 GMT

In this webinar, Leif Schauser, Ph.D., Director Product Management Genome Analysis, will review the latest features in the new QIAGEN CLC Genomics Workbench 20. The following topics will be covered:
• One-click solutions and expert tools for NGS data analysis
• Working with reads from various platforms (Illumina, IonTorrent, Oxford Nanopore, Pacific Biosciences, BGI/MGI)
• Tailored solutions for RNA-seq, DNA-seq and methylation
• Efficient algorithms for read trimming, mapping, de novo assembly and variant calling
• Effective management of reference data
• Scalable processing of many samples, with advanced workflow and reporting capabilities
• Easy installation on Windows, Mac and Linux

Interested in learning more?

Click here

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

Workflow construction and customization using QIAGEN CLC Genomics Workbench

Thu, 22 Feb 2024 08:40:00 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

Batch Renaming Files in CLC Workbench

Tue, 16 Jan 2024 14:10:39 GMT

Add/remove characters from element names or replace parts of names, optionally using regular expressions.

Convert Legacy QIAseq Custom Analyses to v24 with QIAseq Panel Analysis...

Tue, 09 Jan 2024 19:00:00 GMT

Custom analyses created with the Analyze QIAseq Samples tool in versions 23.x and earlier are no longer supported from version 24 onwards. The tool Convert Legacy QIAseq Custom Analyses helps converting custom analyses by creating custom sets and/or pre-configured workflow copies.

QIAseq Panel Analysis Assistance for Standard QIAseq Panels

Mon, 08 Jan 2024 17:25:43 GMT

Introduction to QIAseq Panel Analysis Assistant for Workbench 24 onwards.

How to use the QIAseq Panel Analysis Assistant
Selecting available preconfigured analyses workflows
Run a QIAseq Panel Analysis

QIAseq Panel Analysis Assistance for Custom QIAseq Panels

Mon, 08 Jan 2024 17:24:17 GMT

For custom QIAseq panels, custom files have to be used instead of some standard Reference data elements. By using a suitable analysis workflow from the QIAseq Panel Analysis Assistant, data from custom QIAseq panels/kits can be analyzed by:

Creating a custom reference data containing the imported elements.
Using a workflow copy configured to use these imported elements.

If you are new to the QIAseq Panel Analysis Assistance, please watch the "QIAseq Panel Analysis Assistance for Standard QIAseq Panels" video tutorial first.

Overview of Result Files Created by QIAseq DNA Workflows

Wed, 03 Jan 2024 13:24:03 GMT

This video provides an overview of the result files obtained when running the "Identify QIASeq DNA Somatic Variants" workflow. How to run the workflow is outlined in the tutorial Find Actionable Variants With QIASeq Panels.

Making Use of Workflow Snippets

Wed, 03 Jan 2024 13:23:26 GMT

Different workflows can share a sequence of connected tools between them. To speed up the creation of new workflows, workflow fragments can be stored in snippets and reused.

Modification of Workflows in CLC Genomics Workbench - Part 2

Wed, 03 Jan 2024 13:22:52 GMT

Additional modification options for existing workflows include the removal/addition of tools as well as output files in a workflow. This is the focus of this video.

Modification of Workflows in CLC Genomics Workbench - Part 1

Wed, 03 Jan 2024 13:22:12 GMT

While existing workflows (e.q. Template Workflows) provide a good starting point for data analysis, it is commonly required to tailor data analysis towards specific needs. How parameters can be modified is discussed in this video.

How to Create an Analysis Workflow in CLC Genomics Workbench

Wed, 03 Jan 2024 13:21:36 GMT

Creating analysis pipelines for automation and standardization using the Workflow Editor.

Introduction to Workflows in CLC Genomics Workbench

Wed, 03 Jan 2024 13:21:02 GMT

Introduction to Workflows for the graphical user interface guided construction of bioinformatics analysis pipelines.

Importing Illumina Reads into CLC Genomics Workbench

Wed, 03 Jan 2024 13:20:31 GMT

Importing single and paired end reads. If the organization of Illumina files for import does is not the default, customization of the import is possible using the Custom read structure field.

Downloading Reference Genomes in CLC Genomics Workbench

Wed, 18 Oct 2023 15:21:12 GMT

Find and download commonly used reference data sets provided by QIAGEN and other public resources into CLC Genomics Workbench by using the Reference Data Manager.

Creation of Hybrid Reference Data in CLC Genomics Workbench

Wed, 18 Oct 2023 15:20:35 GMT

In cases where more than one organism is sequenced within one sample, a reference containing all the organisms may be needed. This video will walk you through the steps of creating a hybrid reference dataset.

Setup of Custom Reference Data in CLC Genomics Workbench

Wed, 18 Oct 2023 15:19:39 GMT

Generate and manage individual custom Reference Data Sets with the Reference Data Manager to simplify the configuration of your workflows with regards to reference data inputs.

Importing Reference Data into CLC Genomics Workbench

Wed, 18 Oct 2023 15:18:44 GMT

Import reference data sets located on your hard drive into CLC Genomics Workbench.

Modification of Custom Reference Data in CLC Genomics Workbench

Tue, 17 Oct 2023 09:58:00 GMT

Modifing custom reference data sets with the Reference Data Manager.

Introduction to QIAGEN CLC Genomics Workbench & Getting Started

Thu, 14 Sep 2023 19:31:33 GMT

In this training, we will introduce you to QIAGEN CLC Genomics Workbench, including a live demo of the basic features and main functionalities.
During the training, we’ll cover:
• A general overview of the Workbench user interface
• Easy installation on Windows, Mac and Linux
• Plugin installation, e.g., Biomedical Genomics Analysis plugin
• Reference Data Management
• Working with reads from various NGS platforms
• Running individual tools and workflows
• Batch processing of data
• Data visualization using Track List/Genome Browser
• How to export of data and share workflows
• Q&A

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