quast
Link to section 'Introduction' of 'quast' Introduction
Quast is Quality Assessment Tool for Genome Assemblies.
Note: Running QUAST, please use the command: quast.py metaquast.py'
For more information, please check its website: https://biocontainers.pro/tools/quast and its home page on Github.
Link to section 'Versions' of 'quast' Versions
- 5.0.2
- 5.2.0
Link to section 'Commands' of 'quast' Commands
- quast.py
- metaquast.py
Link to section 'Module' of 'quast' Module
You can load the modules by:
module load biocontainers
module load quast
Link to section 'Example job' of 'quast' 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 Quast on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=quast
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers quast
metaquast.py --gene-finding --threads 8 \
meta_contigs_1.fasta meta_contigs_2.fasta \
-r meta_ref_1.fasta,meta_ref_2.fasta,meta_ref_3.fasta \
-o quast_out_genefinding