segalign
Link to section 'Introduction' of 'segalign' Introduction
Segalign is a scalable GPU system for pairwise whole genome alignments based on LASTZ's seed-filter-extend paradigm.
Docker hub: https://hub.docker.com/r/gsneha/segalign
Home page: https://github.com/gsneha26/SegAlign
Link to section 'Versions' of 'segalign' Versions
- 0.1.2
Link to section 'Commands' of 'segalign' Commands
- faToTwoBit
- run_segalign
- run_segalign_repeat_masker
- segalign
- segalign_repeat_masker
- twoBitToFa
Link to section 'Module' of 'segalign' Module
You can load the modules by:
module load biocontainers
module load segalign
Link to section 'Example job' of 'segalign' 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 segalign on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=segalign
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers segalign