TOGA is a new method that integrates gene annotation, inferring orthologs and classifying genes as intact or lost. TOGA implements a novel machine learning based paradigm to infer orthologous genes between related species and to accurately distinguish orthologs from paralogs or processed pseudogenes. This tutorial explains how to get started using TOGA. It shows how to install and execute TOGA, and how to handle possible issues that may occur.

References:

Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed AW, Kontopoulos DG, Hilgers L, Lindblad-Toh K, Karlsson EK, Zoonomia Consortium, Hiller M.
Integrating gene annotation with orthology inference at scale.
PubMed Science, 2023

• toga GitHub Page

• Module Name: toga (see the modules page for more information)
• Unusual environment variables set
  • TOGA_GENOME toga reference directory
  • TOGA_CONFIG toga config directory
  • TOGA_SUPPLY toga supplymentary directory
  • TOGA_TEST_DATA sample data for running toga

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=4g --gres=lscratch:10 
[user@cn3144 ~]$ module load toga 
[+] Loading java 17.0.3.1  ...
[+] Loading singularity  3.10.5  on cn4292
[+] Loading nextflow 22.10.2
[+] Loading toga  1.1.2

[user@cn3144 ]$ cp -r $TOGA_SUPPLY/* . 

[user@cn3144 ]$ 
toga.py \
        $TOGA_TEST_DATA/hg38.mm10.chr11.chain \
        $TOGA_TEST_DATA/hg38.genCode27.chr11.bed \
        $TOGA_GENOME/hg38.2bit \
        $TOGA_GENOME/mm10.2bit \
        --kt --pn test -i \
        $TOGA_SUPPLY/hg38.wgEncodeGencodeCompV34.isoforms.txt \
        --nc $TOGA_CONFIG \
        --cb 3,5 --cjn 500 --u12 supply/hg38.U12sites.tsv --ms \
	--nextflow_dir ./

Create a batch input file (e.g. toga.sh). For example:

#! /bin/bash

module load toga || exit 1
cp -r $TOGA_SUPPLY/* .

toga.py \
        $TOGA_TEST_DATA/hg38.mm10.chr11.chain \
        $TOGA_TEST_DATA/hg38.genCode27.chr11.bed \
        $TOGA_GENOME/hg38.2bit \
        $TOGA_GENOME/mm10.2bit \
        --kt --pn test -i \
        $TOGA_SUPPLY/hg38.wgEncodeGencodeCompV34.isoforms.txt \
        --nc $TOGA_CONFIG \
        --cb 3,5 --cjn 500 --u12 supply/hg38.U12sites.tsv --ms \
        --nextflow_dir ./

Submit this job using the Slurm sbatch command.

sbatch toga.sh