Difference between revisions of "Bowtie"

Revision as of 17:48, 10 August 2012

Description

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).

Bowtie is a part of the Tuxedo suite.

HPC pre-built Bowtie Indexes are located in /scratch/hpc/bio/bowtie. They should be available for bowtie use automatically. If you have additional indexes that could be of use to UF Biological Community please contact us and we'll add them to the reference file space.

Required Modules

modules documentation

Serial

bowtie

System Variables

HPC_{{#uppercase:bowtie}}_DIR - installation directory
HPC_BOWTIE_BIN - executable directory
HPC_BOWTIE_DOC - documents directory
HPC_BOWTIE_EX - examples directory
HPC_BOWTIE_SCR - scripts directory
0.12.7 - BOWTIE_INDEXES - location of pre-built index files
2.0.0b3 - BOWTIE2_INDEXES - location of pre-built index files
Pre-built Bowtie indexes can be found in the /project/bio/bowtie directory.

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 [[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
-<!-- ########  Template Configuration ######## -->
-<!--Edit definitions of the variables used in template calls
-Required variables:
-app - lowercase name of the application e.g. "amber"
-url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
-Optional variables:
-INTEL - Version of the Intel Compiler e.g. "11.1"
-MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
--->
 {|
 <!--Main settings - REQUIRED-->
 |{{#vardefine:app|bowtie}}
 |{{#vardefine:url|http://bowtie-bio.sourceforge.net/index.shtml}}
-<!--Compiler and MPI settings - OPTIONAL -->
-|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
-|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
-<!--Choose sections to enable - OPTIONAL-->
-|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
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 |{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
 |}
-<!-- ########  Template Body ######## -->
 <!--Description-->
 {{#if: {{#var: url}}|
@@ Line 37: / Line 22: @@
 HPC pre-built Bowtie Indexes are located in ''/scratch/hpc/bio/bowtie''. They should be available for bowtie use automatically. If you have additional indexes that could be of use to UF Biological Community please contact us and we'll add them to the reference file space.
+<!--Modules-->
-==Available Versions==
-* 0.12.7
-* 0.12.8 - Default.
-* 2.2.0-beta3 - will become default when released as a final version.
-* 2.2.0-beta5 - new features since beta3. See [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie2] for details.
-<!-- -->
 ==Required Modules==
 [[Modules|modules documentation]]
 ===Serial===
 *{{#var:app}}
+==System Variables==
+* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
 * HPC_BOWTIE_BIN - executable directory
 * HPC_BOWTIE_DOC - documents directory
@@ Line 55: / Line 36: @@
 * 2.0.0b3 - BOWTIE2_INDEXES - location of pre-built index files
 * Pre-built Bowtie indexes can be found in the <code>/project/bio/bowtie</code> directory.
-{{#if: {{#var: exe}}|==How To Run==
+<!--Additional-->
+{{#if: {{#var: exe}}|==Additional Information==
 |}}
 {{#if: {{#var: conf}}|==Configuration==