bcbio-nextgen protocols

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bcbio-nextgen specifications

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Unique identifier OMICS_01121
Name bcbio-nextgen
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Parallelization MapReduce
License MIT License
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes

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bcbio-nextgen in pipelines

 (4)
2018
PMCID: 5831037
PMID: 29489876
DOI: 10.1371/journal.pone.0192947

[…] clinical data analysis was completed in r (v3.2.4) []., sequencing data quality was assessed using fastqc (v0.11.4) []. sequences were mapped to the human genome (version hsapiens grch37) using the bcbio-nextgen pipeline (v0.9.6a), applying cutadapt (v1.9.1) [], aligning reads with star (v2.5.0c) [], and counting sequences per gene with featurecount (v1.4.4) []. non protein-coding genes […]

2017
PMCID: 5382922
PMID: 28392986
DOI: 10.7717/peerj.3166

[…] the proposed prioritisation framework is fully integrated along with all the tools required to produce the results from raw sequencing data in bcbio (https://github.com/chapmanb/bcbio-nextgen). snpeff 4.3 and later are available at http://snpeff.sourceforge.net/. the prioritisation code for structural variants is accessible […]

2017
PMCID: 5725088
PMID: 29245897
DOI: 10.18632/oncotarget.18502

[…] dbgap (database of genotypes and phenotypes) [], accessions phs000328.v2.p1 and phs000573.v1.p1., alignment and variant calling was performed within the bcbio framework (https://github.com/chapmanb/bcbio-nextgen). reads were aligned to the hg19 human reference genome assembly using bwa [], no realignment or recalibration was performed. duplicate reads were removed from final bam files using […]

2017
PMCID: 5739687
PMID: 29285300
DOI: 10.18632/oncotarget.22413

[…] 3.6) package. somatic point mutations were called with vardict [] algorithms. copy number variations (cnvs) were detected with cnvkit []. the exome sequencing data analysis was implemented by bcbio_nextgen (https://github.com/chapmanb/bcbio-nextgen) pipeline. the annotation of the somatic mutations was implemented using annovar []., about 10 mg frozen tissue per sample was homogenized […]


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bcbio-nextgen in publications

 (14)
PMCID: 5946718
PMID: 29719257
DOI: 10.1016/j.celrep.2018.03.131

[…] harmonic resonance produced as a result of multiphoton microscopy. for more information, see ., sequencing reads were mapped to the mouse mm10 genome using the rna-seq pipeline implemented by the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.io/en/latest/). for more information, see ., kaplan-meier survival analysis was performed and survival between cohorts compared using log-rank […]

PMCID: 5906695
PMID: 29670109
DOI: 10.1038/s41467-018-03828-2

[…] the molecular subtypes of tumors from the icgc cohort were unavailable, but we identified one msi sample from the icgc cohort using msiseq., raw sequencing data was uniformly processed using the bcbio-nextgen pipeline (v0.9.3). briefly, sequencing reads were aligned to the human reference genome (hg19) using bwa. duplicated reads marked by picard were removed. indel regions were realigned […]

PMCID: 5831037
PMID: 29489876
DOI: 10.1371/journal.pone.0192947

[…] clinical data analysis was completed in r (v3.2.4) []., sequencing data quality was assessed using fastqc (v0.11.4) []. sequences were mapped to the human genome (version hsapiens grch37) using the bcbio-nextgen pipeline (v0.9.6a), applying cutadapt (v1.9.1) [], aligning reads with star (v2.5.0c) [], and counting sequences per gene with featurecount (v1.4.4) []. non protein-coding genes […]

PMCID: 5823945
PMID: 29472603
DOI: 10.1038/s41598-018-21727-w

[…] denatured according to illumina guidelines. rna sequencing (rna-seq) was performed using a high output 1 × 76 bp kit on an illumina nextseq 500 platform., rna-seq fastq files were processed using bcbio-nextgen (version 1.0.1) (https://github.com/chapmanb/bcbio-nextgen) where reads were mapped to the human genome build hg38 (grch38.79) using hisat2 (version 2.0.5) yielding between 5.3–20.6 m […]

PMCID: 5639583
PMID: 28985730
DOI: 10.1186/s12920-017-0297-7

[…] (n = 7), peruvian (n = 12), african american (n = 1), lebanese (n = 1), bermudian (n-1), and kuwait (n = 2). ces data were processed using the bcbio pipeline v.0.9.6 (https://github.com/chapmanb/bcbio-nextgen)., genotype calls were first made using the illumina genomestudio software suite. to generate outputs in ped and map formats for downstream analysis in plink, a plink export plug-in […]


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