1. The Bio-Community Perl toolkit for microbial ecology
- Author
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Gene W. Tyson, Florent E. Angly, and Christopher J. Fields
- Subjects
Microbiological Techniques ,Statistics and Probability ,Computer science ,business.industry ,Computational Biology ,File format ,Microbiology ,Applications Notes ,Biochemistry ,Computer Science Applications ,World Wide Web ,Computational Mathematics ,Software ,Computational Theory and Mathematics ,Software Design ,README ,Humans ,Software design ,Perl ,business ,Sequence Analysis ,Molecular Biology ,computer ,Ecosystem ,computer.programming_language - Abstract
Summary: 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. Contact: f.angly@uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics online
- Published
- 2014
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