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Detect horizontal gene transfer events from metagenome data

Zeqian Li

Last updated: May 21st, 2023

This is a work in progress. A Snakemake pipeline to detect different kinds of horizontal gene transfer (HGT) signatures.

Currently includes:

  • Detect mobile gene elements using mobileOG
  • Detect virus using VirSorter2 (follows VirSorter2 SOP)
    • VirSorter2 pass 1
    • CheckV for quality control
    • VirSorter2 pass 2 to prepare annotation
    • Annotation using DRAMv

Usage

Install the following conda environments and packages:

  • mobileog: mobileOG
  • vs2: VirSorter2
  • checkv: CheckV
  • DRAM: DRAM

Run:

  • Change configurations in config/config.yml. See commments in the file.
  • Dry run for testing: snakemake --cores all -n
  • Actual run snakemake --cores all --conda-frontend conda --use-conda -k
  • Use a custom config file: snakemake --cores all --configfile config/config_sag.yml --conda-frontend conda --use-conda -k

Future features:

Future features:

Future improments:

  • Automate database installation
  • Automate Conda installation using yaml configs