tv.qiagenbioinformatics.com

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.

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

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?   

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

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

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

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

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

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

Now, you can access and share the interpretative power of QIAGEN Ingenuity Pathway Analysis (IPA) in an easy-to-consume format – without installing any extra software. IPA Interpret identifies and summarizes the biological themes in your results with the help of AI, creating a shareable, interactive report. You will learn how to:• Create an IPA Interpret report that can be easily shared with others• Gain valuable insight into critical biological pathways, key regulators and more with just a few clicks• Easily customize charts, such as the highly popular volcano bubble chart, taking advantage of new features introduced with recent updates• Export both graphical and tabular results Please make sure you can open the following IPA interpret report for this hands-on workshop:https://analysis.ingenuity.com/ipw/RVy_DS08o_2CDODA-BNBIg Please feel free to reach out to us if you run into any issues.

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

From clinicians to translational researchers to drug developers, everyone is feeling the pressure to match patients with the right therapy faster. The challenge intensifies with rare and inherited diseases, where information is limited and affected individuals are few and scattered across the world. But you can cut weeks from your variant interpretation workflow – without compromising accuracy. On September 24, see how Human Gene Mutation Database (HGMD) Professional can shorten the path to germline variant insights using expert-curated data. Explore almost 30 years of curated variant knowledge, spanning over 17,600 genes and more than 38,000 phenotypes. Learn how you can use HGMD Pro to: • Distinguish clinically significant variants from VUS  • Use batch search vs. advanced search  • Curate genes using HGMD Pro’s accurate, up-to-date information  • Identify the predominant genetic variant in a specific gene to understand the genetic mechanisms underlying associated diseases  • Answer other variant-related questions

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 

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 subtypeOutputs annotated consensus sequences with gene and CDS tracks for intuitive visualizationDetects low-frequency variants that may indicate mixed infectionsPresents 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.

IPA is more than just an analysis program; it can also help you write grants and publications. IPA provides biological insights backed by expert-curated findings and thousands of pre-analyzed multi-omics datasets. You can search for existing knowledge on molecules of interest, build networks and review results from public studies. Or you can identify key pathways, regulatory molecules and functional changes in your results and see how your data relates to published studies. You'll learn how to:• Search IPA’s vast collection of curated literature and omics data• Build your own networks and predict activity changes• Effectively use new features such as IPA Interpret for collaboration and hypothesis generation• Explore a library of over 100,000 precomputed IPA analyses pulled from publicly available studies• Deeply interrogate critical pathways• Predict regulators causing your observed expression changes• Contextualize your results by comparing them to internal and public data• Generate the necessary tables and figures for your manuscript

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

In this webinar, you will learn how to use QIAGEN Ingenuity Pathway Analysis to identify target mRNAs for your miRNAs of interest and associate them with pathways, diseases, biological functions, tissues and cell types.Explore:• How to analyze miRNA-seq datasets alone or together with the corresponding mRNA datasets• How to use QIAGEN IPA without a dataset, using miRNA IDs• An introduction to databases and curated content specific to miRNA• How to effectively apply various filters and functionalities to identify biomarkers, key targets and biological mechanisms

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.

Many QIAGEN Ingenuity Pathway Analysis (IPA) users have expressed strong interest in taking advantage of public single-cell expression data. Such data is readily available and easily accessible in IPA. We are hosting a 1hr training focused on some common use cases related to this topic.You'll learn to:• Easily locate single-cell studies, samples or cell types of interest• Study pathways and networks pertaining to such projects to explore biological and cellular mechanisms• Investigate sample- and cell-level gene expression for biomarker investigation