ArticlePeerJ2017
HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities.
Article in PeerJ, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Kente: A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Leveraging spectrum of graph sheaf Laplacian as a genome-architecture-aware measure of microbiome diversity.bioRxiv : the preprint server for biology · 2026Article
- A machine learning framework for interpreting phylogenetic tree patterns in interkingdom horizontal gene transfer.Frontiers in bioinformatics · 2026Article
- Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.Nature communications · 2025Article
- Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.Bioinformatics (Oxford, England) · 2024Article
- Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs.bioRxiv : the preprint server for biology · 2024Article
- Leveraging comparative genomics to uncover alien genes in bacterial genomes.Microbial genomics · 2023Article
- Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022Review
- Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes.Genome biology and evolution · 2019Review
- MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches.Microbiome · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.