hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Horizontal gene transfer (HGT) is a significant evolutionary mechanism in prokaryotes, insects, and plants.
• The extent and mechanisms of HGT in humans remain largely unexplored, despite evidence of microbial integrations in human studies.
• Existing tools for HGT investigation often lack high levels of automation.

Purpose of the Study:

• To introduce nf-core/hgtseq, a novel, automated bioinformatics pipeline for analyzing HGT from sequencing data.
• To provide a standardized and scalable tool for investigating HGT across different organisms, including humans.
• To facilitate a systematic approach to understanding the role and extent of HGT.

Main Methods:

• Development of a Nextflow-based pipeline, nf-core/hgtseq, adhering to nf-core standards.
• Application of the pipeline to analyze six exome datasets from five mammalian species.
• Ensuring the pipeline's portability and scalability across diverse computing environments.

Main Results:

• Demonstrated the performance of nf-core/hgtseq on mammalian exome data.
• Confirmed the pipeline's ability to run seamlessly in various computational settings.
• Showcased compatibility with existing exome and whole-genome sequencing data.

Conclusions:

• nf-core/hgtseq offers a standardized, automated, and scalable solution for HGT analysis.
• The tool enables researchers to readily investigate HGT in their sequencing data, expanding research scope.
• Facilitates systematic investigation into the open questions surrounding HGT mechanisms, extent, and role in evolution.