minimap2
Link to section 'Introduction' of 'minimap2' Introduction
Minimap2
is a versatile pairwise aligner for genomic and spliced nucleotide sequences.
For more information, please check its website: https://biocontainers.pro/tools/minimap2 and its home page on Github.
Link to section 'Versions' of 'minimap2' Versions
- 2.22
- 2.24
- 2.26
Link to section 'Commands' of 'minimap2' Commands
- minimap2
- paftools.js
- k8
Link to section 'Module' of 'minimap2' Module
You can load the modules by:
module load biocontainers
module load minimap2
Link to section 'Example job' of '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