# bowtie

## Summary

+ **Module Name:** bowtie
+ **Support Level:** Secondary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://bowtie-bio.sourceforge.net/index.shtml](http://bowtie-bio.sourceforge.net/index.shtml)

## Software Description

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns
short DNA sequences (reads) to the human genome at a rate of over 25
million 35-bp reads per hour. Bowtie indexes the genome with a
Burrows-Wheeler index to keep its memory footprint small: typically
about 2.2 GB for the human genome (2.9 GB for paired-end).
## General Linux

To run this software interactively in a Linux environment run the commands:

    module load bowtie
    bowtie ...

For bowtie versions 2.0 and above, use the program "bowtie2" instead of simply "bowtie".

To see a list of available options, type the command:

    bowtie2 -h

Bowtie programs may also be submitted to a queue using a Slurm script such as the one below:

    #SBATCH --nodes=3
    #SBATCH --ntasks-per-node=8
    #SBATCH --mem=1000mb
    #SBATCH --time=8:00:00
    #SBATCH --partition=msismall
    #SBATCH --mail-user=sample_email@umn.edu
    #SBATCH --mail-type=ALL

    module load bowtie

    bowtie2 -p $SLURM_NTASKS reads/e_coli_10000snp.fq ec_snp.sam

Note the use of -p $SLURM_NTASKS; this option is used to specify the number of threads used by Bowtie. Also note that only 0.X versions of Bowtie are available on Agate.