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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.



See versions of bowtie2 which are available:

$ module avail bowtie2

Load and run bowtie2:

$ module load bowtie2/2.3.3
$ bowtie2


Notes from the sysadmin during installation:

$ cd /tmp
$ wget '' -O
$ unzip
$ sudo mkdir /export/apps/bowtie2/2.3.3
sudo cp -rv bowtie2-2.3.3/* /export/apps/bowtie2/2.3.3
bowtie2-software.txt · Last modified: 2017/12/25 21:35 by aorth