====== Bowtie 2======

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.

[[https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#how-is-bowtie-2-different-from-bowtie-1| Differences between Bowtie1 and Bowtie2]].


===== Information =====

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

===== Usage =====

See versions which are available:
<code>$ module avail bowtie2</code>

Load one version into your environment and run it:
<code>$ module load bowtie2/2.5.0
$ bowtie2</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>