MetaBAT

MetaBAT is a tool for the accurate and efficient binning of metagenomic contigs into genome bins (metagenome-assembled genomes) using tetranucleotide frequencies and contig abundances. On Roihu it is provided as MetaBAT2.

• MetaBAT
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

License

Free to use and open source. See the MetaBAT license.

Available

• Roihu: 2.15, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load metabat/2.15

MetaBAT2 takes an assembly and a per-contig depth file (computed from BAM alignments with jgi_summarize_bam_contig_depths):

jgi_summarize_bam_contig_depths --outputDepth depth.txt aln.sorted.bam
metabat2 -i assembly.fa -a depth.txt -o bins/bin -t 8

Example batch script

#!/bin/bash
#SBATCH --job-name=metabat2
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load metabat/2.15

metabat2 -i assembly.fa -a depth.txt -o bins/bin -t $SLURM_CPUS_PER_TASK

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

More information

• MetaBAT repository

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