Software: MetaHipMer (MHM2)
Description
MetaHipMer is a de novo metagenome short-read assembler. Version 2 (MHM2) is written entirely in UPC++ and runs efficiently on both single servers and on multinode supercomputers, where it can scale up to coassemble terabase-sized metagenomes.
Available Versions
| Unspecified: | 2.0.0 |
|---|
Home page: https://bitbucket.org/berkeleylab/mhm2/wiki/Home.md
Commands
- mhm2.py
Module
You can load the modules by:
module load biocontainers
module load mhm2
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run mhm2 on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=mhm2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers mhm2
mhm2.py -r input_1.fastq,input_2.fastq