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).

For reads longer than about 50 bp Bowtie 2 is generally faster, more sensitive, and uses less memory than Bowtie 1. For relatively short reads (e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or more sensitive.

• Version: 1.2.3
• Added: October, 2014
• Updated: April, 2020
• Link: http://bowtie-bio.sourceforge.net/index.shtml

See versions of bowtie which are available:

$ module avail bowtie

Load one version into your environment and run it:

$ module load bowtie/1.2.3
$ bowtie

Notes from the sysadmin during installation:

$ cd /tmp
$ wget 'https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.3/bowtie-1.2.3-linux-x86_64.zip?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie%2F1.2.3%2Fbowtie-1.2.3-linux-x86_64.zip%2Fdownload&ts=1587985836' -O bowtie-1.2.3-linux-x86_64.zip
$ unzip bowtie-1.2.3-linux-x86_64.zip
$ cd bowtie-1.2.3-linux-x86_64
$ sudo mkdir -p /export/apps/bowtie/1.2.3
$ sudo cp -r . /export/apps/bowtie/1.2.3