Qiagen CLC Genomics Workbench
Description
CLC Genomics Workbench (Qiagen) is a graphical user interface (GUI) based bioinformatics software. It houses tools for molecular biology and Next Generation Sequencing (NGS) analysis (see Listing of Analysis Functions below).
Listing of Analysis Functions
Classic Computational Molecular Biology Tools
- Nucleotide analysis
- Convert between DNA and RNA
- Find reverse complement
- Identify open reading frames
- Translate nucleotide sequence to protein sequence
- Predict RNA secondary structure
- Protein analysis
- Predict secondary structure
- Search for domains
- Identify proteolytic cleavage sites
- Create antigenicity, hydrophobicity, and charge plots
- Sequence analysis
- Find motifs and patterns
- Determine sequence composition
- Sequence alignment
- Pairwise and multi-sequence alignments
- BLAST
- Construct phylogenetic trees
- Cloning
- Restriction enzyme mapping
- PCR primers
- Design
- Determine primer properties (melting point, self annealing, secondary structure)
- Identify binding site and PCR product
NGS tasks
- Pre-alignment tasks
- Sequence quality check
- Trimming
- Demultiplexing
- Map sequencing data to reference
- De novo genome assembly
- Color space mapping
- Long read support
DNA sequencing
- Variant detection
- Variant annotation
- Predict functional consequence of variant
Gene expression
- Microarray
- RNA sequencing (can process spike-ins)
- miRNA sequencing
Epigenetics
- ChIP sequencing
- Bisulfite sequencing
Biological insights
- Directly interface with Qiagen Ingenuity Pathway Analysis (IPA) to extract biological insight.
Visualizations
- Genome browser
Information mining
- Download NGS data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA)
- Obtain gene information from NCBI
- Obtain protein structure from PDB and sequences from UniProt
Recommendations
CLC Genomics Workbench and Ingenuity Pathway Analysis (IPA) are developed by Qiagen. Results from CLC Genomics can be imported to IPA for pathways analysis. The combination of CLC Genomics Workbench and IPA allows us to go from a gene level of understanding to understanding biological function and regulatory mechanisms.
Things to Know
Although CLC Genomics Workbench is comprehensive, compute resources on a user's local machine may be a limiting factor for analysis.
Input Data Types
- FASTQ/FQ
- FASTA/FNA/FA
- SAM
- BAM
- VCF
- TXT
- BAS.H5
- BASX.H5
- AB
- ABI
- AB1
- SCF
- PHD
- SFF
- GFF
- GTF
- BED
- WIGGLE
- Tracks/annotations from the UCSC Genome Browser and COSMIC database
We can import data to CLC Genomics Workbench from the following sequencing instruments:
- Illumina
- Oxford Nanopore
- PacBio
- Sanger
- Ion Torrent
Output Data Types
- Visualizations can be exported with varying resolutions as the following:
- PNG
- JPG
- TIF
- SVG
- PS
- EPS
- Tabular data can be exported as:
- CSV
- XLS
- XLSX
- Tab delimited TXT
- HTML
- GFF
- Track graphics
Access Information
You must submit a request through service.cancer.gov to obtain access to CLC Genomics Workbench. This software requires access to a floating license server (three simultaneous users), and so care should be taken to return the license when the software is not actively being used (i.e. close the application). Working with CLC Genomics Workbench requires login to the NIH network or VPN connection if remote.
Getting Help
Documentation for the CLC Genomics Workbench is available under the Help tab in the software. For the CLC Genomics Workbench manual, click here. Additionally, there are tutorials available for different workflows. Finally, Qiagen hosts webinars addressing the use of and updates to this software. To access these videos, click here.