Segalign

Introduction

Segalign is a scalable GPU system for pairwise whole genome alignments based on LASTZ’s seed-filter-extend paradigm.

For more information, please check:
Docker hub: https://hub.docker.com/r/gsneha/segalign
Home page: https://github.com/gsneha26/SegAlign

Versions

  • 0.1.2

Commands

  • faToTwoBit

  • run_segalign

  • run_segalign_repeat_masker

  • segalign

  • segalign_repeat_masker

  • twoBitToFa

Module

You can load the modules by:

module load biocontainers
module load segalign

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 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