CLC Genomics Workbench statistics

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CLC Genomics Workbench specifications


Unique identifier OMICS_01124
Name CLC Genomics Workbench
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 12
Stability Stable
Free trial Yes
Maintained Yes


No version available



  • person_outline CLC Genomics Workbench Team

CLC Genomics Workbench citations


Calreticulin and integrin alpha dissociation induces anti inflammatory programming in animal models of inflammatory bowel disease

Nat Commun
PMCID: 5958137
PMID: 29773794
DOI: 10.1038/s41467-018-04420-4

[…] to determine size distribution and concentration and sequenced on the NextSeq 500 (Illumina) with paired-end 36-base read option. Reads were mapped on mm10 mouse reference genome and quantified using CLC Genomics Workbench version 9.5.1 and 10.1.1 (QIAGEN). RNA-seq data sets are deposited in the NCBI GEO under accession number GSE98407 and GSE109728. […]


Mutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment

Nat Commun
PMCID: 5958119
PMID: 29773874
DOI: 10.1038/s41467-018-04193-w

[…] Sequence reads were mapped against the human reference genome (NCBI build 37/hg19) using CLC Genomics Workbench (version 6.5.1) software (CLC bio). Variants with minor allele frequencies <1% in the dbSNP (Version 137) database were selected and annotated for impact on the encoded protein […]


An epizootic of Chlamydia psittaci equine reproductive loss associated with suspected spillover from native Australian parrots

PMCID: 5953950
PMID: 29765033
DOI: 10.1038/s41426-018-0089-y

[…] ds at the Australian Genome Research Facility (AGRF), Parkville, Australia. Read quality for each sample was assessed with FastQC v.0.11.2, prior to trimming, read mapping, and de novo assembly using CLC Genomics workbench (Qiagen, USA). Initial read mapping to the reference C. psittaci 6BC, as well as Horse_pl chromosomes and plasmids was performed in CLC Genomics to determine the read depth for […]


Predictable Phenotypes of Antibiotic Resistance Mutations

PMCID: 5954217
PMID: 29764951
DOI: 10.1128/mBio.00770-18
call_split See protocol

[…] ccording to the manufacturer’s recommendations. The samples were subjected to whole-genome sequencing using a MiSeq system (Illumina, USA). The paired-end sequence reads were trimmed and mapped using CLC Genomics Workbench (CLC Bio, Denmark) using standard parameters. Subsequently, inversion, deletions, structural variants, and single nucleotide polymorphisms were determined using standard paramet […]


The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites

Sci Rep
PMCID: 5954100
PMID: 29765106
DOI: 10.1038/s41598-018-25981-w

[…] Raw sequences were quality controlled with fastQC. Filtering and assembly was performed in CLC Genomics Workbench (version 6.5.2, CLC bio, Aarhus, Denmark). The contig representing the mitogenome was identified with a BLAST search of the S. magnus mitogenome against all contigs in the assem […]


Novel canine circovirus strains from Thailand: Evidence for genetic recombination

Sci Rep
PMCID: 5951951
PMID: 29760429
DOI: 10.1038/s41598-018-25936-1
call_split See protocol

[…] ystem using MiSeq Reagent kit V3 (300 × 2 cycles). Raw reads were initially screened using an in-house metagenomics pipeline to identify interesting viral reads. Reference assembly was performed with CLC Genomics Workbench 9.0. Phylogenetic analyses were carried out using MEGA 7. […]


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CLC Genomics Workbench institution(s)

CLC Genomics Workbench reviews

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Arup Ghosh

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For wet lab biologists, CLC workbench is a great tool for analyzing next-generation sequencing datasets. Most of the analysis pipelines are predefined, so very less time wasted on setup process. Also one can easily manipulate existing pipelines according to their convenience.


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I've bee using this software for years and I have found its solution as one of the best in the class of bioinformatics workbenches although I have found that its usage is very limited many cases due to the cost of the software that it's licensing represent for many labs. Nonetheless this workbench allows to get a free-limited versio that is still very usefull for doing general sequence visualization and organization tasks. It provides both a Server and a Client implementation so is very scalable and compatible with all main OS.