Minialign

Introduction

Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads.

For more information, please check its website: https://biocontainers.pro/tools/minialign and its home page on Github.

Versions

• 0.5.3

Commands

• minialign

Module

You can load the modules by:

module load biocontainers
module load minialign

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 Minialign on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=minialign
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers minialign

minialign -d index.mai genome.fasta
minialign -l index.mai input.fastq > out.sam