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...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2017-11-01
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| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/4015.pdf |
| _version_ | 1797417954538684416 |
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| author | Weizhi Song Kerrin Steensen Torsten Thomas |
| author_facet | Weizhi Song Kerrin Steensen Torsten Thomas |
| author_sort | Weizhi Song |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T06:25:59Z |
| format | Article |
| id | doaj.art-8e022229d08242b0938f0764d74c469f |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:25:59Z |
| publishDate | 2017-11-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-8e022229d08242b0938f0764d74c469f2023-12-03T11:20:00ZengPeerJ Inc.PeerJ2167-83592017-11-015e401510.7717/peerj.4015HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communitiesWeizhi Song0Kerrin Steensen1Torsten Thomas2Centre for Marine Bio-Innovation, University of New South Wales, Sydney, AustraliaCentre for Marine Bio-Innovation, University of New South Wales, Sydney, AustraliaCentre for Marine Bio-Innovation, University of New South Wales, Sydney, AustraliaThe 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.https://peerj.com/articles/4015.pdfHorizontal gene transferSimulatorBioinformatics |
| spellingShingle | Weizhi Song Kerrin Steensen Torsten Thomas HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities PeerJ Horizontal gene transfer Simulator Bioinformatics |
| 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 | Horizontal gene transfer Simulator Bioinformatics |
| url | https://peerj.com/articles/4015.pdf |
| work_keys_str_mv | AT weizhisong hgtsimasimulatorforhorizontalgenetransferhgtinmicrobialcommunities AT kerrinsteensen hgtsimasimulatorforhorizontalgenetransferhgtinmicrobialcommunities AT torstenthomas hgtsimasimulatorforhorizontalgenetransferhgtinmicrobialcommunities |