Bowtie2¶
Bowtie2 is an ultra fast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Bowtie2 is available as a module on Apocrita.
Usage¶
To run the default version of Bowtie2, simply load the bowtie2 module:
$ module load bowtie2
$ bowtie2 -h
Usage: bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> |
--interleaved <i>} -S [<sam>]
For full usage documentation, run bowtie2 -h.
Example job¶
Serial job¶
Here is an example job using 1 core and 1G memory:
#!/bin/sh
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load bowtie2
# Prepare example genomes in <inputDir>
# Output is stored in <outputDir>
bowtie2-build <inputDir> <outputDir>
bowtie2-inspect <outputDir>