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  • 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.



See versions of bowtie which are available

$ module avail bowtie

Load and run bowtie

$ module load bowtie/1.1.2
$ bowtie


Notes from the sysadmin during installation:

wget "" -O
cd bowtie-1.1.2
sudo mkdir /export/apps/bowtie/1.1.2
sudo cp -r . /export/apps/bowtie/1.1.2/
bowtie-software.txt · Last modified: 2015/07/23 12:58 by joguya