Introduction ~~~~~~~~ Anchorwave is used for sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation.
For more information, please check its website: https://biocontainers.pro/tools/anchorwave and its home page on Github.
- 1.0.1
Commands ~~~~~~~ - anchorwave - gmap_build - gmap - minimap2
You can load the modules by:
module load biocontainers
module load anchorwaveExample 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 Anchorwave on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=anchorwave
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers anchorwave
anchorwave gff2seq -i Zea_mays.AGPv4.34.gff3 -r Zea_mays.AGPv4.dna.toplevel.fa -o cds.fa