Difference between revisions of "Bowtie"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) |
|||
| (22 intermediate revisions by 4 users not shown) | |||
| Line 1: | Line 1: | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]] |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
{| | {| | ||
<!--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}} | ||
| − | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |
| − | |{{#vardefine: | ||
| − | |||
| − | |||
| − | |||
| − | |||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
| Line 27: | Line 13: | ||
|{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | ||
|} | |} | ||
| − | |||
<!--Description--> | <!--Description--> | ||
{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
| − | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | + | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} |
| + | |||
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. | ||
| − | + | ;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 '<code>/data/reference/bowtie</code>' | |
| − | + | ||
| − | + | 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]]. | |
| − | + | ||
| − | + | <!--Modules--> | |
| − | <!-- --> | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | + | ==System Variables== | |
| + | * 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 | ||
| − | * | + | * BOWTIE_INDEXES - pre-built index files directory |
| − | + | <!--Additional--> | |
| − | + | {{#if: {{#var: exe}}|==Additional Information== | |
| − | {{#if: {{#var: exe}}|== | + | 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. |
|}} | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 59: | Line 46: | ||
{{#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 | + | {{#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 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.