Difference between revisions of "BBMap"
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<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_DOC - documentation directory (docs/) | ||
| + | * HPC_{{uc:{{#var:app}}}}_RES - resource directory (resources/) | ||
| + | * HPC_{{uc:{{#var:app}}}}_CONF - configuration directory (config/) | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 17:55, 10 June 2022
Description
This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded.
BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. Very fast.
Environment Modules
Run module spider bbmap to find out what environment modules are available for this application.
System Variables
- HPC_BBMAP_DIR - installation directory
- HPC_BBMAP_BIN - executable directory
- HPC_BBMAP_DOC - documentation directory (docs/)
- HPC_BBMAP_RES - resource directory (resources/)
- HPC_BBMAP_CONF - configuration directory (config/)