Difference between revisions of "Bowtie"

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__NOTOC____NOEDITSECTION__
 
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[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
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[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]]
<!-- ########  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"
 
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{|
 
{|
 
<!--Main settings - REQUIRED-->
 
<!--Main settings - REQUIRED-->
 
|{{#vardefine:app|bowtie}}
 
|{{#vardefine:app|bowtie}}
 
|{{#vardefine:url|http://bowtie-bio.sourceforge.net/index.shtml}}
 
|{{#vardefine:url|http://bowtie-bio.sourceforge.net/index.shtml}}
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
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|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
 
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<!--Description-->
 
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
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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 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.
 
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.
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;Note:
<!--Location-->
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If you are using bowtie we installed you '''do not''' need to specify the path, only the database name. If you are using some other software and must specify the full path use '<code>/data/reference/bowtie</code>'
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
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==Available Versions==
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If you have additional indexes that could be of use to others in the UF community please contact us and we'll add them to the reference file space. You can, of course build your own indexes for your own use, simply pass the path to those indexes in the bowtie command.
* 0.12.7
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* 0.12.8 - Default.
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We provide both [[Bowtie]] and [[Bowtie2]].
* 2.2.0-beta3 - will become default when released as a final version.
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* 2.2.0-beta5 - new features since beta3. See [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie2] for details.
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==Environment Modules==
{{#if: {{#var: mod}}|==Running the application using modules==
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_BOWTIE_BIN - executable directory
 
* HPC_BOWTIE_BIN - executable directory
 
* HPC_BOWTIE_DOC - documents directory
 
* HPC_BOWTIE_DOC - documents directory
 
* HPC_BOWTIE_EX - examples directory
 
* HPC_BOWTIE_EX - examples directory
 
* HPC_BOWTIE_SCR - scripts directory
 
* HPC_BOWTIE_SCR - scripts directory
* 0.12.7 - BOWTIE_INDEXES - location of pre-built index files
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* BOWTIE_INDEXES - pre-built index files directory
* 2.0.0b3 - BOWTIE2_INDEXES - location of pre-built index files
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<!--Additional-->
{{#if: {{#var: exe}}|==How To Run==
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{{#if: {{#var: exe}}|==Additional Information==
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
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Note: If your data is compressed your job script should add another CPU core to the job resource request to accommodate the external gzip process that bowtie will run.
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|}}
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

Latest revision as of 13:06, 15 August 2022

Description

bowtie website  

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.

Note

If you are using bowtie we installed you do not need to specify the path, only the database name. If you are using some other software and must specify the full path use '/data/reference/bowtie'

If you have additional indexes that could be of use to others in the UF community please contact us and we'll add them to the reference file space. You can, of course build your own indexes for your own use, simply pass the path to those indexes in the bowtie command.

We provide both Bowtie and Bowtie2.

Environment Modules

Run module spider bowtie to find out what environment modules are available for this application.

System Variables

  • HPC_BOWTIE_DIR - installation directory
  • HPC_BOWTIE_BIN - executable directory
  • HPC_BOWTIE_DOC - documents directory
  • HPC_BOWTIE_EX - examples directory
  • HPC_BOWTIE_SCR - scripts directory
  • BOWTIE_INDEXES - pre-built index files directory

Additional Information

Note: If your data is compressed your job script should add another CPU core to the job resource request to accommodate the external gzip process that bowtie will run.