General
Learn about the different BLAST searches and options available in the workbench.
QIAGEN CLC Genomics Workbench, QIAGEN CLC Main WorkbenchUse the tools and functionalities of the workbench to simplify your cloning strategy and visualize every steps of the process: Look for restriction enzymes, design primers, and simulate your cloning strategy and results.
QIAGEN CLC Genomics Workbench, QIAGEN CLC Main WorkbenchPredict the secondary structure of an RNA molecule.
QIAGEN CLC Genomics Workbench, QIAGEN CLC Main WorkbenchLearn how to simulate Gateway cloning.
QIAGEN CLC Genomics Workbench, QIAGEN CLC Main WorkbenchLearn how to reconstruct a phylogeny and visualize metadata on the tree.
QIAGEN CLC Genomics Workbench, QIAGEN CLC Main WorkbenchThis tutorial will show you how to link variants to positions on a 3D protein structure, and how to interpret the resulting interactive 3D model. The focus will be on identifying variants associated with drug resistance to chronic myeloid leukemia treatment.
QIAGEN CLC Genomics WorkbenchWorkflows
Create, edit, and manage workflows in your workbench.
QIAGEN CLC Genomics WorkbenchLearn about launching workflows with more than one changing input in batch mode.
QIAGEN CLC Genomics Workbench, QIAGEN CLC Main WorkbenchQuickly create a customized analysis pipeline by editing an existing workflow.
QIAGEN CLC Genomics WorkbenchDe novo assembly
Learn how to manually join or split contigs using the Align Contigs tool of Genome Finishing Module.
QIAGEN CLC Genomics WorkbenchRequired plugin: CLC Genomics Finishing Module (commercial)
This tutorial highlights some of the tools for a typical de novo sequencing workflow with a data set from a high-throughput sequencing machine.
QIAGEN CLC Genomics WorkbenchAn introduction to how to import fastq paired data, run a sequence quality report, trim the data, and run a de novo assembly with scaffolding.
QIAGEN CLC Genomics WorkbenchUsing the Transcript Discovery plugin, quickly annotate de novo the Fragaria vesca genome using both long and short reads.
QIAGEN CLC Genomics WorkbenchPlugin required: Transcript Discovery plugin (non-commercial)
An introduction to the long read tools available in the CLC Genomics Workbench, focusing on hybrid assembly of long, error-prone reads and read polishing with high quality, short reads. Includes assessment of assembly quality, and how and when to perform reassembly of contigs.
QIAGEN CLC Genomics WorkbenchRead mapping and variants
An introduction to processing fastq files to generate variant calls, QC metrics and other results using the CLC LightSpeed Module.
QIAGEN CLC Genomics WorkbenchAn overview of CGP data analysis using the CLC LightSpeed Module, including detecting variants, CNVs, DNA fusions, and generating MSI scores, and TMB scores. Workflow customization to support various types of CGP data is also covered.
QIAGEN CLC Genomics WorkbenchUnderstand the parameters of the Map Reads to Reference tool, and the impact of using paired end data on the mapping results.
QIAGEN CLC Genomics WorkbenchAnalyze targeted sequencing data to detect somatic variants using a template workflow: inspect the resulting QC report and detected variants, assess and optimize recall and precision, and optionally upload results to QCI Interpret for clinical interpretation.
QIAGEN CLC Genomics WorkbenchRequired plugin: Biomedical Genomics Analysis plugin (non-commercial).
Assemble Sanger sequences into contigs to find - and resolve - conflicts between reads.
QIAGEN CLC Genomics Workbench, QIAGEN CLC Main WorkbenchCopy number variants are amplifications and deletions of exon and chromosome fragments as well as whole exons or chromosomes. The copy number variant detection algorithm is designed to detect copy number variations (CNVs) from targeted resequencing experiments. These can be either gene panels or whole exome sequencing. It identifies CNV regions where the normalized coverage of the sample to be analyzed differs from the control samples in a statistically significant way.
QIAGEN CLC Genomics WorkbenchEpigenomics
Analyze bisulfite sequencing data to detect methylated cytosines, identify hypermethylated regions and individual CpG sites, inspect and interpret methylation patterns, and finally automate the entire analysis using a workflow.
QIAGEN CLC Genomics WorkbenchAnalyze a ChIP‐Seq sample to detect significant peaks: perform quality control, visualize peak shapes and associated genes, and extract DNA sequences from the peak regions.
QIAGEN CLC Genomics WorkbenchThis tutorial demonstrates how to build a Methylation Database that is useful for prediction of methylation profiles in mixture samples. The tutorial data set is constructed from cell line samples using the QIAseq T cell Infiltration panel (MHS-202Z)
QIAGEN CLC Genomics WorkbenchRequired plugin: Biomedical Genomics Analysis plugin (non-commercial)
Expression and fusions
Analyze microarray samples from two groups: set up an experiment, perform quality control using MA plots, box plots, PCA plots, and hierarchical clustering, perform statistical analyses to identify and visualize differentially expressed genes, and optionally perform annotation tests.
QIAGEN CLC Genomics Workbench, QIAGEN CLC Main WorkbenchAnalyze RNA-Seq samples and identify differentially expressed genes using template workflows: inspect the resulting QC reports, PCA plots, heat maps, and volcano plots. Optionally upload results to QIAGEN Ingenuity Pathway Analysis (IPA) for biological interpretation.
QIAGEN CLC Genomics Workbench, QIAGEN IPAAnalyze RNA-Seq samples from multiple tissues and timepoints: investigate outliers and structure in the data, identify, visualize and cluster differentially expressed genes, and perform detailed investigation of expression patterns for genes of interest.
QIAGEN CLC Genomics WorkbenchAnalyze an RNA-Seq sample to detect fusions using a template workflow and a Custom Reference Data Set: inspect the resulting QC report, review the support for the identified fusions, and investigate missing fusions.
QIAGEN CLC Genomics WorkbenchRequired plugin: Biomedical Genomics Analysis plugin (non-commercial).
Analyze miRNA samples and identify differentially expressed miRNAs using template workflows: inspect the resulting reports, heat map, and expression browser.
QIAGEN CLC Genomics WorkbenchRequired plugin: Biomedical Genomics Analysis plugin (non-commercial).
This tutorial uses the capabilities of CLC Genomics Workbench with the Biomedical Genomics Analysis plugin to analyse UPX 3' reads and assess quality. It includes steps for demultiplexing, mapping and metadata handling, as well as downstream analysis options.
QIAGEN CLC Genomics WorkbenchRequired plugin: Biomedical Genomics Analysis plugin (non-commercial)
Immune repertoire
Analyze samples to detect clonotypes using a template workflow: inspect the resulting QC report, review the immune repertoire properties, and perform comparisons across samples.
QIAGEN CLC Genomics WorkbenchRequired plugin: Biomedical Genomics Analysis plugin (non-commercial)
Oncology
This tutorial will guide you through the process of identifying somatic variants from a matched tumor/normal sample pair from one patient using the Biomedical Genomics Analysis plugin.
QIAGEN CLC Genomics WorkbenchRequired plugin: Biomedical Genomics Analysis plugin (non-commercial).
Calculate Tumor Mutational Burden (TMB) and Microsatellite Instability (MSI) using a template workflow and review the results.
QIAGEN CLC Genomics WorkbenchRequired plugin: Biomedical Genomics Analysis plugin (non-commercial).
This tutorial demonstrates how a template workflow can be configured to calculate a Homologue Recombination Deficiency (HRD) score by adding the tool Calculate LOH and HRD Score (beta).
QIAGEN CLC Genomics WorkbenchRequired plugin: Biomedical Genomics Analysis plugin (non-commercial).
Microbial genomics
Assemble metagenomes derived from two different groups of samples and investigate their functional differences.
QIAGEN CLC Genomics WorkbenchRequired plugins: CLC Microbial Genomics Module (commercial)
This tutorial will take you through the tools available in CLC Microbial Genomics Module to perform typing and epidemiological study of cultured bacteria using the metadata functionalities of the Microbial Genomics module.
QIAGEN CLC Genomics WorkbenchRequired plugin: CLC Microbial Genomics Module (commercial)
This tutorial will take you through the different tools available in CLC Microbial Genomics Module and CLC Genomics Workbench to perform OTU clustering and estimate alpha and beta diversities of microbial communities with the Microbial Genomics module.
QIAGEN CLC Genomics WorkbenchPlugin required: CLC Microbial Genomics Module (commercial)
Learn how to identify individual constituents of a microbial community, and how to identify microbiome profiles that can be associated with certain sample parameters (metadata). In this example we solve a forensics case where the microbiome of the soil on a suspects boots can be associated with the soil microbiome at a crime scene.
QIAGEN CLC Genomics WorkbenchRequired plugin: CLC Microbial Genomics Module (commercial)
Learn how easy it is to monitor the evolution of a microbiota over time using the taxonomic profiling tools from CLC Microbial Genomics Module.
QIAGEN CLC Genomics WorkbenchPlugin required: CLC Microbial Genomics Module (commercial)
Learn how CLC Genomics Module can analyze metagenomics samples with respect to the presence and abundance of antimicrobial resistance (AMR) with the Drug Resistance Analysis tools and accompanying databases, in particular the integrated up-to-date QIAGEN Microbial Insight - Antimicrobial Resistance database (QMI-AR).
QIAGEN CLC Genomics WorkbenchPlugin required: CLC Microbial Genomics Module (commercial)
Create a custom MLST scheme for ad hoc outbreak analysis: identify best reference(s), create an MLST scheme and use it to type reads, investigate and visualize typing results.
QIAGEN CLC Microbial Genomics ModulePlugin required: CLC Microbial Genomics Module (commercial)
Learn how to use the Update Sequence Attribute in Lists tool to annotate sequence lists to create your own microbial reference data for use in various downstream analyses.
QIAGEN CLC Genomics WorkbenchPlugin required: CLC Microbial Genomics Module (commercial)
Use the tools in CLC Microbial Genomics Module to analyze viral hybrid capture panel data. Learn how to identify viral strains in a sample and potential virus integration events into a host genome.
QIAGEN CLC Genomics WorkbenchRequired plugin: CLC Microbial Genomics Module (commercial)
Analyze metatranscriptomic Oxford Nanopore MinION reads from SARS-CoV-2 samples using the long read tools available in CLC Genomics Workbench.
QIAGEN CLC Genomics WorkbenchSingle cell
This tutorial uses the CLC Genomics Workbench and CLC Single Cell Analysis Module to focus on one of the main areas when conducting single cell RNA-Seq analysis: performing cell type prediction and overlaying the information on Dimensionality Reduction Plots.
QIAGEN CLC Genomics WorkbenchRequired plugins: CLC Single Cell Analysis Module (commercial).
This tutorial uses the CLC Genomics Workbench and CLC Single Cell Analysis Module to reanalyze published data and recreate the results. You will learn to import different data types, perform QC and normalization, and using the flexible coloring and highlighting functionality of the UMAP plot. The included workflow provides everything needed for RNA velocity analysis, including the creation of a list of velocity genes, as well as a browsable phase portrait plot.
QIAGEN CLC Genomics WorkbenchRequired plugins: CLC Single Cell Analysis Module (commercial).