Software: Megahit
Description
Megahit is a ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
Available Versions
| Unspecified: | 1.2.9 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/megahit and its home page on Github.
Commands
- megahit
Module
You can load the modules by:
module load biocontainers
module load megahit
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 Megahit on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=megahit
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers megahit
megahit --12 SRR1976948.abundtrim.subset.pe.fq.gz,SRR1977249.abundtrim.subset.pe.fq.gz -o combined