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.

There is no upper limit on read length in Bowtie 2. Bowtie 1 had an upper limit of around 1000 bp.

Differences between Bowtie1 and Bowtie2.

• Version: 2.5.0
• Added: March, 2015
• Updated: November, 2022
• Link: https://bowtie-bio.sourceforge.net/bowtie2/index.shtml

See versions which are available:

$ module avail bowtie2

Load one version into your environment and run it:

$ module load bowtie2/2.5.0
$ bowtie2

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://liquidtelecom.dl.sourceforge.net/project/bowtie-bio/bowtie2/2.5.0/bowtie2-2.5.0-linux-x86_64.zip
$ unzip bowtie2-2.5.0-linux-x86_64.zip
$ sudo cp -r bowtie2-2.5.0-linux-x86_64/* /export/apps/bowtie2/2.5.0