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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




No version available



  • 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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