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

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

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

Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.

Bowtie2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB.

Bowtie2 supports gapped, local, and paired-end alignment modes.

show all versions of bowtie2

$ module avail bowtie2

---------------------------------------------------------------------------------------------- /etc/modulefiles/ilri ----------------------------------------------------------------------------------------------
bowtie2/2.1.0 bowtie2/2.2.2 bowtie2/2.2.3

load specific version, e.g. v2.2.3:

$ module load bowtie2/2.2.3

get help:

$ bowtie2 --help

bowtie2 is precompiled already, so all you have to do is copy the binaries to export-apps

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/

create module file:

#%Module1.0
#####################################################################
##
## bowtie2 Modulefile
## by James Oguya, j.oguya@cgiar.org
## October, 2014
##

set appname         bowtie2
set version         2.2.3
set prefix          /export/apps/${appname}/${version}
set exec_prefix     ${prefix}
set url "http://bowtie-bio.sourceforge.net"
set msg "Bowtie2 is an ultrafast & memory-efficient tool for aligning sequencing reads to long reference sequences. Its particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.\n\nBowtie Official Site: $url\n"

proc ModulesHelp { } {
    puts stderr "$msg"
}

module-whatis   "$msg"

conflict        bowtie2

prepend-path    PATH    ${exec_prefix}

as always, push to github & let ansible take care of teh rest!

ansible-playbook compute.yml --limit=compute --tags=modules -K