Bowtie2 v2.2.1

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. Bowtie 2 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. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Module file

The module file can be found in this location:

 /cm/shared/modulefiles/SHARED/

<source lang='tcl'>

1. %Module1.0#######################################################################
   1. bowtie2-2.2.1 modulefile

proc ModulesHelp { } {

       puts stderr "\tAdds bowtie2-2.2.1 to your environment"

}

module-whatis "Adds bowtie2-2.2.1 to your environment"

set bowtie2_2_2_1_root /cm/shared/apps/SHARED/bowtie/bowtie2-2.2.1/

prepend-path PATH $bowtie2_2_2_1_root

</source>

Installation details

The pre-compiled binaries were downloaded from SourceForge on 15-03-2014:

  http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.1/

This included the GapCloser software (v1.12) and ErrorCorrection (v0.04)

See also

• Globally installed software
• ABGC specific modules

External links

• Bowtie2 home page
• Bowtie2 Manual
• SourceForge link for GapCloser

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