Bpipe statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool Bpipe
info

Tool usage distribution map

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

Associated diseases

info

Popular tool citations

chevron_left Read alignment Differential expression Libraries/frameworks File indexation Adapter trimming Variant detection chevron_right
Want to access the full stats & trends on this tool?

Bpipe specifications

Information


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
Version 0.9.9.5
Stability Stable
Maintained Yes

Download


download.png
conda.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Simon Sadedin

Additional information


http://docs.bpipe.org/

Publication for Bpipe

Bpipe citations

 (10)
call_split

Investigating reproducibility and tracking provenance – A genomic workflow case study

2017
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 […]

library_books

Gene length and detection bias in single cell RNA sequencing protocols

2017
F1000Res
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) ( ). […]

library_books

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

2016
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 […]

library_books

Human genome meeting 2016

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 […]

library_books

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

2016
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 […]

library_books

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

2016
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 […]


Want to access the full list of citations?
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

Bpipe reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Bpipe