Cactus

Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111

Usage

Version	module name
1.2.3	cactus/1.2.3
1.3.0	cactus/1.3.0

cactus <jobStorePath> <seqFile> <outputHal> --binariesMode singularity --maxCores <number of cpus>

Example: /share/Apps/examples/cactus

#!/bin/bash

#SBATCH -p debug
#SBATCH -n 16
#SBATCH -N 1
#SBATCH -t 90
#SBATCH -J cactus

module load cactus/1.3.0

cd ${SLURM_SUBMIT_DIR}

cactus jobStore examples/evolverMammals.txt examples/evolverMammals.hal --root mr --binariesMode singularity --maxCores ${SLURM_NTASKS}

More Information: https://github.com/ComparativeGenomicsToolkit/cactus