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).
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
Pre-built bowtie indexes for popular genomes are available at
Bowtie programs may also be submitted to a queue using PBS script such as the one below:
#PBS -l nodes=3:ppn=8,pmem=1000mb,walltime=8:00:00
#PBS -m abe

module load bowtie

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

Note the use of -p $PBS_NP; 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 Itasca and Cascade.

Compatibility issues:
Bowtie genome indexes built using 0.X versions are not compatible with indexes built using 2.X versions.  Significant changes (improvements) have been made to Bowtie command-line options, and to how Bowtie performs alignments.  To see a list of installed Bowtie versions type the command
module show bowtie
Bowtie 0.X genome indexes are available at
Additional Information
Support level: 
Software category: