Difference between revisions of "BWA"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replace - "Usage policy" to "Usage Policy") |
|||
| (5 intermediate revisions by one other user not shown) | |||
| Line 1: | Line 1: | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]] | [[Category:Software]][[Category:Bioinformatics]][[Category:NGS]] | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
{| | {| | ||
<!--Main settings - REQUIRED--> | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|bwa}} | |{{#vardefine:app|bwa}} | ||
|{{#vardefine:url|http://bio-bwa.sourceforge.net/}} | |{{#vardefine:url|http://bio-bwa.sourceforge.net/}} | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
|{{#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--> | ||
| Line 34: | Line 20: | ||
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. | ||
<!--Modules--> | <!--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_BWA_BIN - executable directory | * HPC_BWA_BIN - executable directory | ||
* HPC_BWA_MAN - manpage directory | * HPC_BWA_MAN - manpage directory | ||
* HPC_BWA_DOC - documentation directory | * HPC_BWA_DOC - documentation directory | ||
| − | {{#if: {{#var: exe}}|== | + | <!--Additional--> |
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 17:07, 10 June 2022
Description
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates.
Environment Modules
Run module spider bwa to find out what environment modules are available for this application.
System Variables
- HPC_BWA_DIR - installation directory
- HPC_BWA_BIN - executable directory
- HPC_BWA_MAN - manpage directory
- HPC_BWA_DOC - documentation directory