Software: Minimap2
Description
Minimap2 is a versatile pairwise aligner for genomic and spliced nucleotide sequences.
Available Versions
Unspecified: | 2.22 2.24 2.26 |
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For more information, please check its website: https://biocontainers.pro/tools/minimap2 and its home page on Github.
Commands
- minimap2
- paftools.js
- k8
Module
You can load the modules by:
module load biocontainers
module load minimap2
Example job
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 Minimap2 on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=minimap2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers minimap2
minimap2 -ax sr Wuhan-Hu-1.fasta \
seq_1.fastq seq_2.fastq \
> aln.sam