HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities

The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce defined HGT within a microbial communi...

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Detalles Bibliográficos
Autores principales: Song, Weizhi, Steensen, Kerrin, Thomas, Torsten
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2017
Materias:
Bioinformatics
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681852/
https://www.ncbi.nlm.nih.gov/pubmed/29134153
http://dx.doi.org/10.7717/peerj.4015
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author Song, Weizhi
Steensen, Kerrin
Thomas, Torsten
author_facet Song, Weizhi
Steensen, Kerrin
Thomas, Torsten
author_sort Song, Weizhi
collection PubMed
description The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce defined HGT within a microbial community. Here, we present HgtSIM, a pipeline to simulate HGT event among microbial community members with user-defined mutation levels. It was developed for testing and benchmarking pipelines for recovering HGTs from complex microbial datasets. HgtSIM is implemented in Python3 and is freely available at: https://github.com/songweizhi/HgtSIM.
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spelling pubmed-56818522017-11-13 HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities Song, Weizhi Steensen, Kerrin Thomas, Torsten PeerJ Bioinformatics The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce defined HGT within a microbial community. Here, we present HgtSIM, a pipeline to simulate HGT event among microbial community members with user-defined mutation levels. It was developed for testing and benchmarking pipelines for recovering HGTs from complex microbial datasets. HgtSIM is implemented in Python3 and is freely available at: https://github.com/songweizhi/HgtSIM. PeerJ Inc. 2017-11-08 /pmc/articles/PMC5681852/ /pubmed/29134153 http://dx.doi.org/10.7717/peerj.4015 Text en ©2017 Song et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Song, Weizhi
Steensen, Kerrin
Thomas, Torsten
HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities
title HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities
title_full HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities
title_fullStr HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities
title_full_unstemmed HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities
title_short HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities
title_sort hgtsim: a simulator for horizontal gene transfer (hgt) in microbial communities
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681852/
https://www.ncbi.nlm.nih.gov/pubmed/29134153
http://dx.doi.org/10.7717/peerj.4015
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AT steensenkerrin hgtsimasimulatorforhorizontalgenetransferhgtinmicrobialcommunities
AT thomastorsten hgtsimasimulatorforhorizontalgenetransferhgtinmicrobialcommunities

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