• 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 & Bowtie2

• Version: 2.2.3
• Added: October, 2014
• Link: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

$ module avail bowtie2

$ module load bowtie2/2.2.3
$ bowtie2

Notes from the sysadmin during installation:

wget "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.3/bowtie2-2.2.3-linux-x86_64.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie2%2F2.2.3%2F&ts=1413528357&use_mirror=tenet" -O bowtie2-2.2.3-linux-x86_64.zip
unzip bowtie2-2.2.3-linux-x86_64.zip
sudo mkdir /export/apps/bowtie2/2.2.3/
sudo cp -rv bowtie2-2.2.3/* /export/apps/bowtie2/2.2.3/