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

Weizhi Song; Kerrin Steensen; Torsten Thomas

doi:10.7717/peerj.4015

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

PeerJ. 2017 Nov 8:5:e4015. doi: 10.7717/peerj.4015. eCollection 2017.

Authors

Weizhi Song^{1

2}, Kerrin Steensen^{1

3}, Torsten Thomas^{1

4}

Affiliations

¹ Centre for Marine Bio-Innovation, University of New South Wales, Sydney, Australia.
² School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
³ Department of Genomic and Applied Microbiology, Georg-August Universität Göttingen, Göttingen, Germany.
⁴ School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia.

Abstract

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.

Keywords: Bioinformatics; Horizontal gene transfer; Simulator.

Grants and funding

This research was funded by the Australian Research Council. Weizhi Song was funded by the China Scholarship Council (201508200019). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.