title: The Bio-Community Perl toolkit for microbial ecology.
abstract: 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.
authors.affiliation: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, Level 5, Molecular Biosciences Building (76), The University of Queensland, Brisbane St Lucia, QLD 4072, Australia and HPCBio, Carver Biotechnology Center, Institute for Genomic Biology, 1206 West Gregory Drive | MC-195, Urbana, IL 61801, USA.
authors.forename: Florent E
authors.initials: FE
authors.lastname: Angly
authors.affiliation: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, Level 5, Molecular Biosciences Building (76), The University of Queensland, Brisbane St Lucia, QLD 4072, Australia and HPCBio, Carver Biotechnology Center, Institute for Genomic Biology, 1206 West Gregory Drive | MC-195, Urbana, IL 61801, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Fields
authors.affiliation: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, Level 5, Molecular Biosciences Building (76), The University of Queensland, Brisbane St Lucia, QLD 4072, Australia and HPCBio, Carver Biotechnology Center, Institute for Genomic Biology, 1206 West Gregory Drive | MC-195, Urbana, IL 61801, USA.
authors.forename: Gene W
authors.initials: GW
authors.lastname: Tyson
mesh_terms: D019295:Computational Biology / Q000379:methods; D017753:Ecosystem; D006801:Humans; D008828:Microbiological Techniques; D008829:Microbiology; D012985:Software Design