Difference between revisions of "BBMap"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
Johnbullard (talk | contribs) |
||
| Line 38: | Line 38: | ||
==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== | ||
Revision as of 20:30, 25 May 2021
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.
Required Modules
Serial
- bbmap
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/)