The Bio-Community Perl toolkit for microbial ecology | Zendy

Florent Angly | Zendy; Christopher J. Fields | Zendy; Gene W. Tyson | Zendy

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The Bio-Community Perl toolkit for microbial ecology

Author(s) -

Florent Angly,

Christopher J. Fields,

Gene W. Tyson

Publication year - 2014

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btu130

Subject(s) - perl , computer science , software , microbial ecology , world wide web , metagenomics , mit license , software engineering , ecology , programming language , biology , biochemistry , bacteria , gene , genetics

The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio-Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio-Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software. Availability an implementation: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A readme file describes software installation and how to contribute.

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