hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer

Abstract

Horizontal gene transfer (HGT) is well described in prokaryotes: it plays a crucial role in evolution, and has functional consequences in insects and plants. However, less is known about HGT in humans. Studies have reported bacterial integrations in cancer patients, and microbial sequences have been detected in data from well-known human sequencing projects. Few of the existing tools for investigating HGT are highly automated. Thanks to the adoption of Nextflow for life sciences workflows, and to the standards and best practices curated by communities such as nf-core, fully automated, portable, and scalable pipelines can now be developed. Here we present nf-core/hgtseq to facilitate the analysis of HGT from sequencing data in different organisms. We showcase its performance by analysing six exome datasets from five mammals. Hgtseq can be run seamlessly in any computing environment and accepts data generated by existing exome and whole-genome sequencing projects; this will enable researchers to expand their analyses into this area. Fundamental questions are still open about the mechanisms and the extent or role of horizontal gene transfer: by releasing hgtseq we provide a standardised tool which will enable a systematic investigation of this phenomenon, thus paving the way for a better understanding of HGT.

Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements

“…Several pipelines for MGE identification have been published recently, such as PathoFact ( de Nies et al, 2021 ), MobileElementFinder ( Johansson et al, 2021 ), MGEFinder ( Durrant et al, 2020 ), VRProfile2 ( Wang et al, 2022 ), MetaCompare ( Oh et al, 2018 ) and hgtSeq ( Carpanzano et al, 2022 ). However, many of the existing tools (MobileElementFinder, MGEFinder, VRprofile2 and hgtSeq) were developed for sequencing data from bacterial isolates, often without being applicable to metagenomics (MobileElementFinder, MGEFinder, hgtSeq).…”