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Protocols

BioPig specifications

Information


Unique identifier OMICS_01225
Name BioPig
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Shell (Bash)
Parallelization MapReduce
Computer skills Advanced
Version 2.0
Stability Stable
High performance computing Yes
Maintained Yes

Download


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Versioning


No version available

Maintainer


  • person_outline Zhong Wang

Additional information


https://github.com/JGI-Bioinformatics/biopig

Publication for BioPig

BioPig citations

 (3)
library_books

A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data

2015
GigaScience
PMCID: 4455317
PMID: 26045962
DOI: 10.1186/s13742-015-0058-5

[…] wtie [], or through a generic adaptor like Hadoop Streaming library) regular Linux applications cannot generally be used directly on it. Two interesting frameworks to simplify scripting in Hadoop are BioPig [] and SeqPig [], which are both built on top of the Apache Pig framework and are capable of automatically distributing data and parallelizing tasks.At the moment, however, Hadoop is incompatib […]

library_books

Applications of the MapReduce programming framework to clinical big data analysis: current landscape and future trends

2014
BioData Min
PMCID: 4224309
PMID: 25383096
DOI: 10.1186/1756-0381-7-22

[…] he solution. Moreover additional tuning of the local Hadoop configuration towards the genome comparison is expected to yield additional performance benefits. A bioinformatics processing tool known as BioPig has been built on the Apache’s Hadoop system and the Pig Latin data flow language []. Compared with traditional algorithms, BioPig has three major advantages: first, BioPig programmability redu […]

call_split

Genetic characterization of Uruguayan Pampa Rocha pigs with microsatellite markers

2014
Genet Mol Biol
PMCID: 4415558
PMID: 25983624
DOI: 10.1590/S1415-475738120140146
call_split See protocol

[…] breeds were included in the study: Berkshire, Celtic, Duroc, Iberian, Landrace, Large White, Meishan and Pietrain, to a total of 415 individuals. Information about these breeds was obtained from the BIOPIG Consortium’s database of the Iberoamerican Porcine Biodiversity Project. This consortium is part of the Red CONBIAND. These data have previously been published by , , and . BIOPIG consortium a […]

Citations

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BioPig institution(s)
Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA; Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
BioPig funding source(s)
Supported in part by the Office of Science of the U.S., Department of Energy under (Contract No. DE-AC02- 05CH112 and DE-AC02-05CH11231).

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