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Tutorials

Introduction


An introduction to workflows

Create, edit, and manage workflows in your workbench.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Assemble sequences to a reference

Assemble Sanger sequences into contigs to find - and resolve - conflicts between reads.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Main Workbench

BLAST searches

Learn about the different BLAST searches and options available in the workbench.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Main Workbench

Visualize variants on protein structure

This 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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Phylogenic trees and metadata

Learn how to reconstruct a phylogeny and visualize metadata on the tree.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Main Workbench

Molecular biology basics

Use 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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Main Workbench

Gateway cloning

Facilitate your Gateway cloning work with the Vector NTI Import plugin.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Main Workbench

Required plugin: Vector NTI Import (non-commercial)

Folding RNA molecules

Learn how to predict the secondary structure of an RNA molecule.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Main Workbench

Running workflows with two inputs in batches

Learn about launching workflows with more than one changing input in batch mode.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Main Workbench

Next generation sequencing


Bisulfite sequencing

Find methylated cytosines and identify regions with high methylation levels in your sequencing reads.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

ChIP sequencing

This tutorial takes you through a complete ChIP sequencing workflow using CLC Genomics Workbench.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Resequencing analysis using tracks

Find and annotate cancer specific variants by comparing normal and cancer tissue reads and by filtering for variants leading to amino acid changes.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Reference genome and annotation tracks

Learn how to create a reference genome and manage track lists to visualize your data and associated annotations.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Read mapping in detail

Understand the parameters of the Map Reads to Reference tool, and the impact of using paired end data on the mapping results.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Comparative analysis of three bovine genomes

Learn how to identify species-specific variants, filter those leading to amino acid changes, and associate relevant species-specific pathways.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

CLC Genome Finishing Module - using the Align Contigs tool

Learn how to manually join or split contigs using the Align Contigs tool of Genome Finishing Module.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Required plugin: CLC Genomics Finishing Module (commercial)

De novo assembly and BLAST

This tutorial highlights some of the tools for a typical de novo sequencing workflow with a data set from a high-throughput sequencing machine.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

De novo assembly of paired data

An introduction to how to import fastq paired data, run a sequence quality report, trim the data, and run a de novo assembly with scaffolding.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

De Novo Transcript Discovery using Long and Short Reads

Using the Transcript Discovery plugin, quickly annotate de novo the Fragaria vesca genome using both long and short reads.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Plugin required: Transcript Discovery plugin (non-commercial)

De novo assembly using long reads and short read polishing

An introduction to the functionality of the Long Read Support plugin, 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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Analysis of SARS-CoV-2 using MinION sequences

Analyze metatranscriptomic Oxford Nanopore MinION reads from SARS-CoV-2 samples using the functionality of the Long Read Support plugin and other CLC Genomics Workbench tools.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Expression analysis


Microarray-based expression analysis

Perform data quality control, identify differentially expressed genes, and interpret your results in a biological context using annotations. This tutorial is based on microarray data but many tools are applicable to RNA-seq.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Main Workbench

Expression analysis using RNA-Seq data

Discover the powerful statistical analysis tools in CLC Genomics Workbench.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Advanced RNA-Seq analysis with upload to IPA

This tutorial demonstrates how workflows can be used to analyze RNA-Seq data efficiently, including submission of expression results to Ingenuity Pathway Analys (IPA) for downstream analysis and interpretation.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

RNA-Seq analysis with four tissues and six timepoints

Analyze 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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Biomedical research


Identification of variants in a tumor sample

This tutorial will guide you through the process of identifying variants and verifying them using Biomedical Genomics Analysis plugin.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Required plugin: Biomedical Genomics Analysis plugin (non-commercial).

Identification of somatic variants in a matched tumor-normal pair

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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Required plugin: Biomedical Genomics Analysis plugin (non-commercial).

Find very low frequency variants with QIAGEN GeneRead Panels

This tutorial uses the capacities of Biomedical Genomics Analysis plugin to find very low frequency variants in targeted amplicon sequences generated using a QIAGEN GeneRead DNAseq Targeted Panels V2 kit.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Required plugin: Biomedical Genomics Analysis plugin (non-commercial).

Copy number variant detection

Copy 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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Find actionable variants with QIAseq Panels

This tutorial uses the capacities of the Biomedical Genomics Analysis plugin to find actionable variants - even at very low frequencies - in Targeted Amplicons sequences generated using a BRCA1 and BRCA2 QIAseq panel kit.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Required plugin: Biomedical Genomics Analysis plugin (non-commercial).

Fusion Detection Using QIAseq RNAscan Panels

This tutorial uses the capacities of the Biomedical Genomics Analysis plugin to detect fusion events in sequences generated using a QIAseq Targeted RNAscan Panel.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Required plugin: Biomedical Genomics Analysis plugin (non-commercial).

miRNA Quantification

Compare differential expression of miRNA between Adrenal Myelolipoma (benign neoplasm) and Adrenocortical Carcinoma to identify miRNA that can be used for diagnostic.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Compare TMB Scores and MSI Statuses from QIAseq Tumor Mutational Burden Panels

This tutorial uses the capabilities of CLC Genomics Workbench with the Biomedical Genomics Analysis plugin to calculate reliable and consistent TMB score and MSI status values from reads sequenced with the QIAseq Tumor Burden Mutation panel assay (DHS-8800Z).

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Find fusion events and variants with QIAseq Multimodal Panels

This tutorial uses the capacities of the Biomedical Genomics Analysis plugin to detect fusion events and find actionable variants in reads generated using a custom QIAseq Multimodal panel.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Modify a workflow to detect specific low frequency variants

In this tutorial, we modify a ready-to-use QIAseq analysis workflow to detect KIT D816V down to a low frequency, illustrating how an existing workflow can be efficiently used as the basis for customized analysis pipelines.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Quantify gene expression using QIAseq UPX 3' panels

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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Required plugin: Biomedical Genomics Analysis plugin (non-commercial)

Immune Repertoire Analysis using QIAseq Immune Repertoire panels

This tutorial uses the capacities of the Biomedical Genomics Analysis plugin to identify clonotype distribution in individual samples and compare immune repertoire across samples.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Required plugin: Biomedical Genomics Analysis plugin (non-commercial)

How to Configure a Workflow to Calculate an HRD Score

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).

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Required plugin: Biomedical Genomics Analysis plugin (non-commercial).

Creating a Methylation Database for Three Cell Types

This 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)

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Required plugin: Biomedical Genomics Analysis plugin (non-commercial)

Microbial genomics


Whole metagenome functional analysis

Assemble metagenomes derived from two different groups of samples and investigate their functional differences.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Microbial Genomics Module

Required plugins: CLC Microbial Genomics Module (commercial), MetaGeneMark (commercial)

Typing and epidemiological clustering of common pathogens

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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Microbial Genomics Module

Required plugin: CLC Microbial Genomics Module (commercial)

OTU clustering step by step

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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Microbial Genomics Module

Plugin required: CLC Microbial Genomics Module (commercial)

OTU clustering using workflows

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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Microbial Genomics Module

Required plugin: CLC Microbial Genomics Module (commercial)

Taxonomic profiling of whole shotgun metagenomic data

Learn how easy it is to monitor the evolution of a microbiota over time using the taxonomic profiling tools from CLC Microbial Genomics Module.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Microbial Genomics Module

Plugin required: CLC Microbial Genomics Module (commercial)

Antibiotic Resistance Analysis

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).

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Microbial Genomics Module

Plugin required: CLC Microbial Genomics Module (commercial)

Working with MLST schemes

This tutorial covers the use of the MLST scheme tools, focusing on scheme creation, visualization, and isolate typing.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Microbial Genomics Module

Plugin required: CLC Microbial Genomics Module (commercial)

Updating and using attributed sequences list as microbial reference data

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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Microbial Genomics Module

Plugin required: CLC Microbial Genomics Module (commercial)

Analysis of Viral Hybrid Panel Data and Identification of Viral Integration Sites

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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench, QIAGEN CLC Microbial Genomics Module

Required plugin: CLC Microbial Genomics Module (commercial)

Single-cell analysis


Train a cell type classifier for single cell RNA-Seq analysis

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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Required plugins: CLC Single Cell Analysis Module (commercial).

Perform Single Cell RNA Expression and Velocity Analysis

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.

Available as a PDF tutorial

QIAGEN CLC Genomics Workbench

Required plugins: CLC Single Cell Analysis Module (commercial).