gfastats
Link to section 'Introduction' of 'gfastats' Introduction
gfastats is a single fast and exhaustive tool for summary statistics and simultaneous fa (fasta, fastq, gfa [.gz]) genome assembly file manipulation. gfastats also allows seamless fasta<>fastq<>gfa[.gz] conversion. It has been tested in genomes even >100Gbp.
BioContainers: https://biocontainers.pro/tools/gfastats
Home page: https://github.com/vgl-hub/gfastats
Link to section 'Versions' of 'gfastats' Versions
- 1.2.3
Link to section 'Commands' of 'gfastats' Commands
- gfastats
Link to section 'Module' of 'gfastats' Module
You can load the modules by:
module load biocontainers
module load gfastats
Link to section 'Example job' of 'gfastats' 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 gfastats on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=gfastats
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers gfastats
gfastats input.fasta -o gfa