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Biomedical Genomics Workbench specifications


Unique identifier OMICS_28761
Name Biomedical Genomics Workbench
Alternative name CLC Cancer Research Workbench
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 5.0.1
Stability Stable
Free trial Yes
Maintained No


No version available



This tool is not available anymore.

Additional information

Biomedical Genomics Workbench citations


Importance of Comprehensive Molecular Profiling for Clinical Outcome in Children With Recurrent Cancer

PMCID: 5920151
PMID: 29732366
DOI: 10.3389/fped.2018.00114

[…] ration Kit and Agilent's SureSelectXT Clinical Research Exome kit. Paired-end sequencing was performed on Illumina instruments, with an average coverage of 50–100×. Data were processed using Qiagen's Biomedical Genomics Workbench and Ingenuity Variant Analysis. RNA sequencing was performed using Illumina's TruSeq Stranded Total RNA Library Prep Kit and paired-end sequencing was performed to gain a […]


Whole exome sequencing identifies mTOR and KEAP1 as potential targets for radiosensitization of HNSCC cells refractory to EGFR and β1 integrin inhibition

PMCID: 5915060
PMID: 29719593
DOI: 10.18632/oncotarget.24266
call_split See protocol

[…] Whole exome sequencing (WES) raw data of cell lines were mapped against human genome reference sequence (hg19-Ensembl) using CLC Biomedical Genomics Workbench v.3.51 (Qiagen, Aarhus, Denmark) (CLC BMW) with following parameters: match score 1; mismatch cost 2; affine gap cost (Insertion/deletion open cost 6; insertion/deletion […]


Relaxin reverses inflammatory and immune signals in aged hearts

PLoS One
PMCID: 5773192
PMID: 29346407
DOI: 10.1371/journal.pone.0190935
call_split See protocol

[…] Raw transcript data was imported into Biomedical Genomics Workbench 3.0.1 and reads were mapped to the rat reference genome. Differentially expressed genes (DEGs) used in pathway analysis were determined between old and young rats with an […]


Loss of activity mutation in the cardiac chloride bicarbonate exchanger AE3 causes short QT syndrome

Nat Commun
PMCID: 5700076
PMID: 29167417
DOI: 10.1038/s41467-017-01630-0
call_split See protocol

[…] instructions (Illumina) followed by hybridization using Nimblegen SeqCap EZ Exome v3 (Roche) and Paired-end Sequencing (2 × 100 bp) on the Illumina HiSeq 2000 with TruSeq v3 chemistry (Illumina). CLC BioMedical Genomics Workbench 2.1.1 (Qiagen) was used for data analysis and data was trimmed for adaptor sequence and ambiguous bases before alignment to GRCh37, duplicate removal and SNV and indel ca […]


Dupuytren’s and Ledderhose Diseases in a Family with LMNA Related Cardiomyopathy and a Novel Variant in the ASTE1 Gene

PMCID: 5753070
PMID: 29104234
DOI: 10.3390/cells6040040

[…] s since fibroblast were not available. The WES studies used enrichment by Agilent SureSelect XT Human All Exon V5 library and paired-end sequencing by Illumina HiSeq2500 at 100X coverage. The CLC bio Biomedical Genomics Workbench v3.5 (Qiagen, Valencia, CA, USA) was used to align the data to the human genome reference (hg38). The Identify and Annotate Variants (WES-HD) workflow and variant analysi […]


Transcription factors and stress response gene alterations in human keratinocytes following Solar Simulated Ultra Violet Radiation

Sci Rep
PMCID: 5648893
PMID: 29051608
DOI: 10.1038/s41598-017-13765-7

[…] l of 0.6 billion reads were obtained from 16 RNA samples with an average of 38.2 million reads per sample. More than 90% of reads were mapped to human genome (Hg38). Data analysis was performed using Biomedical Genomics Workbench version 3.5.3 (Qiagen). Differential gene expression was analyzed using Advance RNA-seq plug-in tool (Qiagen) by comparing each treated group versus corresponding control […]


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