Nextalign

Introduction

Nextalign is a viral genome sequence alignment tool for command line.

Versions

  • 1.10.3

Commands

  • nextalign

Module

You can load the modules by:

module load biocontainers
module load nextalign

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 Nextalign on our clusters:

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

module --force purge
ml biocontainers nextalign

nextalign \
     --sequences data/sars-cov-2/sequences.fasta \
     --reference data/sars-cov-2/reference.fasta \
     --genemap data/sars-cov-2/genemap.gff \
    --genes E,M,N,ORF1a,ORF1b,ORF3a,ORF6,ORF7a,ORF7b,ORF8,ORF9b,S \
    --output-dir output/ \
    --output-basename nextalign