Difference between revisions of "Applications/Minimap2"
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[username@login01 ~]$ module add minimap2/2.15 | [username@login01 ~]$ module add minimap2/2.15 | ||
| + | </pre> | ||
| + | |||
| + | ===Batch Job=== | ||
| + | <!-- Example from: https://hpc.nih.gov/apps/minimap2.html --> | ||
| + | <pre> | ||
| + | #!/bin/bash | ||
| + | #SBATCH -J minimap2job | ||
| + | #SBATCH -p compute | ||
| + | #SBATCH -n 4 | ||
| + | #SBATCH -o %N.%j.out | ||
| + | #SBATCH -e %N.%j.err | ||
| + | |||
| + | module purge | ||
| + | module load minimap2/2.15 | ||
| + | |||
| + | minimap2 -ax map10k $MINIMAP2_HOME/test/MT-human.fa $MINIMAP2_HOME/test/MT-orang.fa > test.sam | ||
</pre> | </pre> | ||
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* [https://github.com/lh3/minimap2 https://github.com/lh3/minimap2] | * [https://github.com/lh3/minimap2 https://github.com/lh3/minimap2] | ||
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Latest revision as of 10:44, 17 November 2022
Application Details
- Description: Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
- Version: 2.15
- Modules: minimap2/2.15
- Citing: If you use minimap2 in your work, please cite: Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. doi:10.1093/bioinformatics/bty191
Usage Examples
Usage information can be found at https://github.com/lh3/minimap2
[username@login01 ~]$ module add minimap2/2.15
Batch Job
#!/bin/bash #SBATCH -J minimap2job #SBATCH -p compute #SBATCH -n 4 #SBATCH -o %N.%j.out #SBATCH -e %N.%j.err module purge module load minimap2/2.15 minimap2 -ax map10k $MINIMAP2_HOME/test/MT-human.fa $MINIMAP2_HOME/test/MT-orang.fa > test.sam