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

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

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


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:


Bioinformatics; Horizontal gene transfer; Simulator

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