CLC Genomics Workbench statistics

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Citations per year

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Popular tool citations

chevron_left Read quality control Genome assembly Read alignment CNV detection SNV detection Alignment evaluation Bioinformatics workflows Phylogenetic network construction Peak calling Adapter trimming Indel detection Assembly evaluation Differentially methylated region detection Methylation annotation chevron_right
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CLC Genomics Workbench specifications

Information


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 10
Stability Stable
Free trial Yes
Maintained Yes

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Maintainer


  • person_outline CLC Genomics Workbench Team <>

CLC Genomics Workbench in pipelines

 (619)
2018
PMCID: 5756330
PMID: 29304737
DOI: 10.1186/s12864-017-4415-x

[…] length of 2 × 75 bases were generated. primary transcriptome libraries were sequenced in single read mode with a read length of 35 or 75 bases., read processing and mapping was carried out with the clc genomics workbench (qiagen aarhus a/s). reads were trimmed by removing adapter sequences using the trim sequences tool and filtered for phred quality scores <30 []. reads from primary […]

2018
PMCID: 5758643
PMID: 29311719
DOI: 10.1038/s41598-017-18445-0

[…] 0.11.3) and overall quality was improved by trimming the reads using trimmomatic, with following parameters: crop = 95, headcrop = 10, minlen = 85., high quality rna-seq reads were mapped using the clc genomics workbench (v. 9.5.3)., traces of ribosomal rna contamination were removed from all libraries by mapping against sunflower ribosomal sequences downloaded from the ncbi database […]

2018
PMCID: 5760739
PMID: 29317509
DOI: 10.1128/mBio.01678-17

[…] sequencing libraries were prepared from 0.2 to 0.9 μg of total rna with the truseq stranded mrna library preparation kit (illumina). the illumina nextseq 500 sequencer was used for sequencing. clc genomics workbench 9 (qiagen) was used to map the rna-seq fastq reads to the human reference genome (hg19). differential expression analysis was performed using the deseq2 package in r () using […]

2018
PMCID: 5764924
PMID: 29326200
DOI: 10.1128/genomeA.01143-17

[…] extraction method () and sequenced using the illumina hiseq 2500 platform at genotech (daejeon, republic of korea). in total, 15,682,948 reads (1,583,977,748 bp) were trimmed and assembled using clc genomics workbench version 6.5.1 (qiagen, netherlands). open reading frame (orf) prediction and annotation were conducted using glimmer version 3.02 (), prodigal version 1.20 (), genemarks […]

2018
PMCID: 5764929
PMID: 29326205
DOI: 10.1128/genomeA.01354-17

[…] using the illumina hiseq 2500 platform. about 1,282,954 short reads were generated with a mean 3,478-fold coverage of the genome. the resulting sequences were de novo assembled using the clc genomics workbench version 8.5.1. the contig sequences were corrected with pilon version 1.11 () and linked using the sspace premium scaffolder version 2.3 (). gapped regions within the scaffolds […]


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CLC Genomics Workbench in publications

 (3802)
PMCID: 5959919
PMID: 29777105
DOI: 10.1038/s41467-018-04256-y

[…] (https://www.arabidopsis.org/) was used as the reference sequence for mapping and variant detection. furthermore, sequenced reads of taqed plant genome were mapped using commercial software (clc genomics workbench v.8.5; qiagen). these variants were also called using this software, with variant-detection workflow shown in supplementary fig. ., to detect the rearrangements induced […]

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

[…] the dss alone group. to further investigate differentially expressed genes (fdr; p < 0.05, fold change > 2) among the three groups, we performed pairwise comparisons of rna-seq data using the clc genomics workbench software. as shown in supplementary fig. , in comparison with the control, 5570 (3483 up- and 2087 downregulated) unique genes were significantly changed in the dss-induced […]

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

[…] 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 […]

PMCID: 5952423
PMID: 29764461
DOI: 10.1186/s12985-018-0998-3

[…] cdna library construction. the samples were sequenced on the illumina nextseq sequencing platform with 15-sample bar-coded multiplexing., analyses of total sequence reads were performed using the clc genomics workbench 9.5.2 platform (https://www.qiagenbioinformatics.com/). the raw reads were filtered to remove the failed reads, and qualified reads were assembled de novo into contigs […]

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

[…] 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 […]


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CLC Genomics Workbench reviews

 (2)
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Arup Ghosh

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Desktop
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.

salvador_angel

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Desktop
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.