Bpipe statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Bpipe

Tool usage distribution map

This map represents all the scientific publications referring to Bpipe per scientific context
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Associated diseases


Popular tool citations

chevron_left Read alignment Differential expression Libraries/frameworks File indexation Adapter trimming Variant detection chevron_right
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Bpipe specifications


Unique identifier OMICS_02301
Name Bpipe
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Groovy, Java, Shell (Bash)
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Maintained Yes




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  • person_outline Simon Sadedin

Additional information


Publication for Bpipe

Bpipe citations


Investigating reproducibility and tracking provenance – A genomic workflow case study

BMC Bioinformatics
PMCID: 5508699
PMID: 28701218
DOI: 10.1186/s12859-017-1747-0
call_split See protocol

[…] g pipelines on remote servers without requiring access to GUI so that they are easily administered through source code management tools []. However, the command line based pipeline frameworks such as bpipe [], Snakemake [] and Ruffus [] used to develop these systems are not flexible enough to support integration of new user-defined steps and analysis tools. Working with such systems requires exper […]


Gene length and detection bias in single cell RNA sequencing protocols

PMCID: 5428526
PMID: 28529717
DOI: 10.5256/f1000research.12181.r22376

[…] 8/bigZips. Reads were summarised across genes using featureCounts (v1.5.0-p3) ( ), with GENCODE M9 annotation for mouse and GENCODE V22 annotation for human datasets. This pipeline was constructed in Bpipe (v0.9.9.3) ( ), and a report summarising the steps produced using MultiQC (v0.8) ( ). […]


Towards agile large scale predictive modelling in drug discovery with flow based programming design principles

J Cheminform
PMCID: 5123367
PMID: 27942268
DOI: 10.1186/s13321-016-0179-6

[…] rts a REST-interface [] that can be used to provide this type of programmability, but this requires interfacing the tool with external scripts outside of the tool itself.Snakemake [], NextFlow [] and BPipe [] are text-based tools implemented as Domain Specific Languages (DSL). DSLs are mini-languages created specifically for the need of a specific domain [], such as the topic at hand, scientific w […]


Human genome meeting 2016

Hum Genomics
PMCID: 4896275
PMID: 27294413
DOI: 10.1186/s40246-016-0063-5

[…] this work, we present a shared, open source analysis pipeline that was developed to meet these needs. Methods To enable a single solution for many different diseases and laboratories, we employed the Bpipe pipeline platform which allows for analysis stages to be easily added, substituted, replaced or customized on a per-sample or per-disease basis. Bpipe also offers powerful features for paralleli […]


Reference genotype and exome data from an Australian Aboriginal population for health based research

Sci Data
PMCID: 4828942
PMID: 27070114
DOI: 10.1038/sdata.2016.23

[…] nome Resource Facility (AGRF). The data was processed using GATK according to GATK Best Practices recommendations, and using the GATK 2.8 data bundle for hg19; the full pipeline was implemented using Bpipe (see Code availability). Briefly, sequences were aligned to the hg19 reference genome with BWA-MEM, followed by the removal of PCR duplicates, base quality score recalibration, indel realignment […]


Comparative assessment of methods for the fusion transcripts detection from RNA Seq data

Sci Rep
PMCID: 4748267
PMID: 26862001
DOI: 10.1038/srep21597

[…] is the latest pipeline that we used for this benchmark study. It uses several external softwares, mainly Bpipe, Velvet, Oases, SAMtools, Bowtie2, BLAT, Dedupe, Reformat, and R packages, for the detection of fusions. This pipeline runs in three modes: 1) ‘assembly’ mode, which assembles the short reads in […]

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Bpipe institution(s)
Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia; Victorian Life Sciences Computation Initiative, The University of Melbourne, Carlton, VIC, Australia

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