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chevron_left Read quality control SNP detection Known transcript quantification Bioinformatics workflows Bioinformatics workflows Bioinformatics workflows Novel transcript quantification Adapter trimming Reference-based transcriptome assembly Bioinformatics workflows Spliced read alignment Bioinformatics workflows Alignment-free transcript quantification chevron_right

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bcbio-nextgen specifications


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 citations


CSF1R+ Macrophages Sustain Pancreatic Tumor Growth through T Cell Suppression and Maintenance of Key Gene Programs that Define the Squamous Subtype

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 […]


Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers

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 […]


Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men

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 […]


Bronchial extracellular matrix from COPD patients induces altered gene expression in repopulated primary human bronchial epithelial cells

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 […]


Renal oncocytoma characterized by the defective complex I of the respiratory chain boosts the synthesis of the ROS scavenger glutathione

PMCID: 5739687
PMID: 29285300
DOI: 10.18632/oncotarget.22413
call_split See protocol

[…] 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 […]


Clinical utility of the low density Infinium QC genotyping Array in a genomics based diagnostics laboratory

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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