Difference between revisions of "Sambamba"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
|||
| Line 22: | Line 22: | ||
[http://lomereiter.github.io/sambamba/docs/sambamba-view.html Sambamba Documentation] | [http://lomereiter.github.io/sambamba/docs/sambamba-view.html Sambamba Documentation] | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | < | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{uc:{{#var:app}}}}_DIR | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 69: | Line 59: | ||
<!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
| − | |||
| − | |||
Revision as of 20:19, 10 June 2022
Description
Sambamba is a high performance modern robust and fast tool for working with SAM and BAM files. Sambamba is written in the D programming language and because of efficient use of modern multicore CPUs it is usually much faster than samtools. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.
Environment Modules
Run module spider sambamba to find out what environment modules are available for this application.
System Variables
- HPC_SAMBAMBA_DIR - installation directory