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bowtie1-software

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.
  • There is no upper limit on read length in Bowtie 2. Bowtie 1 had an upper limit of around 1000 bp.

Bowtie v1.1.1

Usage

  • show all versions of bowtie
    $ module avail bowtie
    
    ---------------------------------------------------------------------------------------------- /etc/modulefiles/ilri ----------------------------------------------------------------------------------------------
    bowtie/0.12.7 bowtie/0.12.8 bowtie/1.0.0  bowtie/1.0.1  bowtie/1.1.1  bowtie2/2.1.0 bowtie2/2.2.2 bowtie2/2.2.3
  • load a specific version, e.g. v1.1.1:
    $ module load bowtie/1.1.1
  • get quick help:
    $ bowtie --help

Installation

  • bowtie comes already compiled, so all you have to do is unzip & copy to export-apps
    wget "http://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.1.1/bowtie-1.1.1-linux-x86_64.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie%2F1.1.1%2F&ts=1413524287&use_mirror=tenet" -O bowtie-1.1.1-linux-x86_64.zip
    unzip bowtie-1.1.1-linux-x86_64.zip
    sudo mkdir /export/apps/bowtie/1.1.1/
    sudo cp -r bowtie-1.1.1/* /export/apps/bowtie/1.1.1/
  • create module file:
    #%Module1.0
    #####################################################################
    ##
    ## bowtie Modulefile
    ## By James Oguya, j.oguya@cgiar.org
    ## October, 2014
    ##
    
    set appname         bowtie
    set version         1.1.1
    set prefix          /export/apps/${appname}/${version}
    set exec_prefix     ${prefix}
    set url "http://bowtie-bio.sourceforge.net"
    set msg "bowtie is an ultrafast, memory-efficient short read aligner that aligns DNA sequences(reads) to the human at 25 million 35-bp reads per hour.\nBowtie Official Site: $url\n"
    
    module-whatis $msg
    
    proc ModulesHelp { } {
        puts stderr "$msg"
    }
    
    conflict        bowtie
    
    prepend-path    PATH    ${exec_prefix}
  • push the new module using ansible
    ansible-playbook compute.yml --limit=compute --tags=modules -K
bowtie1-software.txt · Last modified: 2014/10/17 10:47 by joguya