Bowtie2 v2.2.1: Difference between revisions
(Created page with " '''[http://soap.genomics.org.cn/soapdenovo.html#intro2 SOAPdenovo2]''' is a popular genome assembler. == Module file == The module file can be found in this location: /cm...") |
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'''[http:// | '''[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml 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. | ||
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The pre-compiled binaries were downloaded from SourceForge on 15-03-2014: | The pre-compiled binaries were downloaded from SourceForge on 15-03-2014: | ||
http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.1/ | http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.1/ | ||
== See also == | == See also == | ||
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== External links == | == External links == | ||
* [http:// | * [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2 home page] | ||
* [http://sourceforge.net/ | * [http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml Bowtie2 Manual] | ||
Latest revision as of 22:59, 15 March 2014
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'>
- %Module1.0#######################################################################
- 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/