Winnowmap¶
Introduction¶
Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences.
For more information, please check:
BioContainers: https://biocontainers.pro/tools/winnowmap
Home page: https://github.com/marbl/Winnowmap
Versions¶
2.03
Commands¶
winnowmap
Module¶
You can load the modules by:
module load biocontainers
module load winnowmap
Example job¶
Warning
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 winnowmap on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=winnowmap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers winnowmap
winnowmap -W repetitive_k15.txt \
-ax map-pb Cm.contigs.fasta \
SRR3982487.fastq > output.sam