megahit
Link to section 'Introduction' of 'megahit' Introduction
Megahit
is a ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
For more information, please check its website: https://biocontainers.pro/tools/megahit and its home page on Github.
Link to section 'Versions' of 'megahit' Versions
- 1.2.9
Link to section 'Commands' of 'megahit' Commands
- megahit
Link to section 'Module' of 'megahit' Module
You can load the modules by:
module load biocontainers
module load megahit
Link to section 'Example job' of 'megahit' Example job
Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
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