MetaBAT2
MetaBAT2 is a tool for metagenome binning.
Availability
| Cluster | Module/Version |
|---|---|
| BOSE | metabat2/2.17 |
| BGSC | N/A |
Note: You can simply use module load metabat2 to activate the most recently installed version of this software.
Arguments / Options
This is a list of arguments for the metabat2 command that we wanted to highlight. Use this online man page for a full list.
| Option | Description |
|---|---|
| --help | Print the help message |
| --inFile | Contigs in fasta format (required) |
| --outFile | Base file and path for each output bin. Default fasta format. |
| --seed | For reproducibility. Defaults to 0 (randoms seed). |
Sample Slurm Script
submit.sh
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]
# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32 # How many CPU cores do you want to request
#SBATCH --nodes=1 # How many nodes do you want to request
# -- SCRIPT COMMANDS -- #
# Load the needed modules
module load metabat2/2.17 # Load metabat2
runMetaBat.sh assembly.fa *.bam
Real Example
Has your research group used MetaBAT2 in a project? Contact the HPC Team and we'd be glad to feature your work.
Citation
Please include the following citation in your papers to support continued development of MetaBAT2.
Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, Wang Z. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019 Jul 26;7:e7359. doi: 10.7717/peerj.7359. PMID: 31388474; PMCID: PMC6662567.