Difference between revisions of "Applications/Minimap2"

From HPC
Jump to: navigation , search
m
m (Batch Job)
 
(3 intermediate revisions by the same user not shown)
Line 15: Line 15:
 
[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>
  
Line 21: Line 37:
 
* [https://github.com/lh3/minimap2 https://github.com/lh3/minimap2]
 
* [https://github.com/lh3/minimap2 https://github.com/lh3/minimap2]
  
 
+
{{Modulepagenav}}
==Navigation==
 
 
 
* [[Main_Page|Home]]
 
* [[Applications|Application support]] *
 
* [[General|General]]
 
* [[Programming|Programming support]]
 

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

Further Information





Modules | Main Page | Further Topics