The Bio-Community Perl toolkit for microbial ecology

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 BioPe...

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Detalles Bibliográficos
Autores principales: Angly, Florent E., Fields, Christopher J., Tyson, Gene W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071200/
https://www.ncbi.nlm.nih.gov/pubmed/24618462
http://dx.doi.org/10.1093/bioinformatics/btu130
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author Angly, Florent E.
Fields, Christopher J.
Tyson, Gene W.
author_facet Angly, Florent E.
Fields, Christopher J.
Tyson, Gene W.
author_sort Angly, Florent E.
collection PubMed
description 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
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spelling pubmed-40712002014-06-26 The Bio-Community Perl toolkit for microbial ecology Angly, Florent E. Fields, Christopher J. Tyson, Gene W. Bioinformatics Applications Notes 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 Oxford University Press 2014-07-01 2014-03-10 /pmc/articles/PMC4071200/ /pubmed/24618462 http://dx.doi.org/10.1093/bioinformatics/btu130 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Angly, Florent E.
Fields, Christopher J.
Tyson, Gene W.
The Bio-Community Perl toolkit for microbial ecology
title The Bio-Community Perl toolkit for microbial ecology
title_full The Bio-Community Perl toolkit for microbial ecology
title_fullStr The Bio-Community Perl toolkit for microbial ecology
title_full_unstemmed The Bio-Community Perl toolkit for microbial ecology
title_short The Bio-Community Perl toolkit for microbial ecology
title_sort bio-community perl toolkit for microbial ecology
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071200/
https://www.ncbi.nlm.nih.gov/pubmed/24618462
http://dx.doi.org/10.1093/bioinformatics/btu130
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