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:

• Tycheposons detection
• Better viral curation

Future improments:

• Automate database installation
• Automate Conda installation using yaml configs