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bowtie-software

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Bowtie

  • 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.

Information

Usage

See versions of bowtie which are available

$ module avail bowtie

Load and run bowtie

$ module load bowtie/1.1.2
$ bowtie

Installation

Notes from the sysadmin during installation:

wget "http://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.1.2/bowtie-1.1.2-linux-x86_64.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie%2F1.1.2%2F&ts=1437645027&use_mirror=liquidtelecom" -O bowtie-1.1.2-linux-x86_64.zip
unzip bowtie-1.1.2-linux-x86_64.zip
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