gapseq

gapseq performs informed prediction and analysis of bacterial metabolic pathways and produces gap-filled genome-scale metabolic models from genome sequences.

gapseq

License

Free to use and open source under GNU GPLv3.

Available

Roihu: 2.1.0, via the bio-apps module.

Usage

gapseq is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the gapseq module:

module load bio-apps/v202603
module load gapseq/2.1.0

Reference sequence database

gapseq requires a reference sequence database for sequence searches. If a shared database is not available on Roihu, download it to a writable location such as your project's /scratch directory.

For bacterial genomes:

DB=/scratch/<project>/gapseq_db

gapseq update-sequences \
    -t Bacteria \
    -D "$DB"

For archaeal genomes, replace Bacteria with Archaea.

Specify the same database directory with -D when running gapseq.

Running gapseq

The full pipeline (pathway prediction, network building and gap-filling) can be run on a genome with the doall subcommand:

gapseq doall genome.fna.gz

Individual steps (find, find-transport, draft, fill) can also be run separately. gapseq analyses can be computationally heavy and should be run as batch jobs:

#!/bin/bash
#SBATCH --job-name=gapseq
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=12:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load gapseq/2.1.0

DB=/scratch/<project>/gapseq_db

gapseq doall \
    -K "$SLURM_CPUS_PER_TASK" \
    -D "$DB" \
    genome.fna.gz

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk