Bpipe protocols

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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 in pipeline

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

[…] 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) ( )., our gene filtering strategy was identical between datasets. genes that had more than 90% zeroes across […]

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Bpipe in publications

PMCID: 5744013
PMID: 29312018
DOI: 10.3389/fpsyt.2017.00291

[…] with a field of view of 256 mm, repetition time of 22 ms, echo time of 9.2 ms, and flip angle of 30°., t1-weighted mr images were converted to the minc file format and processed using the minc-bpipe-library pre-processing pipeline from the cobra laboratory tools. pre-processing consisted of a two-step whole-scan bias field correction, with and without an approximate brain mask using n4itk […]

PMCID: 5718432
PMID: 29211727
DOI: 10.1371/journal.pone.0187779

[…] to neuroanatomy that measures differences in the local density of brain tissue through a voxel-wise comparison of multiple brain images []. mri images were run through a bioinformatics pipeline (bpipe). the images were first corrected for intensity non-uniformity (shading artifacts) using the n4 software package [] and then spatially normalized by linear transformation using icbm 152 atlases […]

PMCID: 5607223
PMID: 28931838
DOI: 10.1038/s41598-017-11883-w

[…] in the isolation map of the suit pipeline located in the anterior cerebellum., prior to the cerebellar parcellation with the maget brain pipeline, we preprocessed (https://github.com/cobralab/minc-bpipe-library) the t1 images and performed n4 correction, cutneck and registration to the mni space using the advanced normalization tools (ants) software. the maget brain pipeline uses five high […]

PMCID: 5575239
PMID: 28851912
DOI: 10.1038/s41598-017-08351-w

[…] (ge medical systems, milwaukee, wi)., all t1-weighted mri data were converted to the minc file format (http://www.bic.mni.mcgill.ca/servicessoftware/minc) and underwent preprocessing using the bpipe tools from the cobra laboratory (https://github.com/cobralab/minc-bpipe-library). this process included rigid (6-parameter) registration to mni space, cropping of the neck region to improve […]

PMCID: 5508699
PMID: 28701218
DOI: 10.1186/s12859-017-1747-0

[…] 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 […]

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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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