Software: Nextalign
Description
Nextalign is a viral genome sequence alignment tool for command line.
Available Versions
| Unspecified: | 1.10.3 |
|---|
Docker hub: https://hub.docker.com/r/nextstrain/nextalign and its home page: https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextalign-cli.html.
Commands
- nextalign
Module
You can load the modules by:
module load biocontainers
module load nextalign
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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