CLC bio pipeline

CLC bio specifications


Unique identifier OMICS_01124
Name CLC bio
Alternative 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 10
Stability Stable
Free trial Yes
Maintained Yes


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  • person_outline CLC Genomics Workbench Team <>

CLC bio citations

PMCID: 5794944

[…] were selected, resulting in a total of 1,050,018 reads (303,493,887 bp). reads were first assembled into contigs using spades version 3.5.0 (8); then, the contigs were further manually joined using clc genomics workbench version 8 by alignment against reference genomes (genbank accession numbers cp000462 and cp005966). the assembled genomes were assessed using quast version 3.0 (9)., […]

PMCID: 5794955

[…] was sent for sequencing on the illumina miseq platform at the universidade católica de brasília (ucb)., the raw reads (6,862,788 million paired-end reads) were trimmed and de novo assembled using clc genomics workbench version 8.0. the resulting contigs were compared to the viral refseq database available in genbank using a blastx search (7) implemented in geneious version 9.1.5 (7). […]

PMCID: 5862824

[…] more than two ambiguous nucleotides were trimmed according to clc procedures. subsequently, adapter sequences were removed according to the illumina adapter list. rna-seq analysis was performed in clc genomics workbench 8.0 by mapping the trimmed reads to the tair10 arabidopsis reference genome sequence, under default settings. reads per kilobase (of exon) per million (rpkm) mapped reads […]

PMCID: 5878828

[…] site were crucial to retain the reads from each sample. following the sorting of reads to each individual sample, the 12 bp barcode on the 5′ end was trimmed and the reads were imported into the clc genomics workbench v9.0 (qiagen, boston, ma, usa). trimmed reads from each sample were mapped to the fragaria vesca genome v2.0.a1 (fvb)34. parameters for read alignment were set at a mismatch […]

PMCID: 5938774

[…] with a minimum coverage of 40–120-fold. we prepared libraries with the nextera xt dna sample preparation kit (illumina) and de novo assembled whole-genome sequence contigs for each strain by using clc genomics workbench version 7.5.1 (qiagen, valencia, ca, usa)., we initially investigated the position of the strains from spain and the united kingdom on the global phylogeny of v. […]

CLC bio 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.