Difference between revisions of "Samblaster"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
|||
| Line 22: | Line 22: | ||
When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs. | When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs. | ||
<!--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 - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| Line 70: | Line 60: | ||
<!--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 20:34, 10 June 2022
Description
samblaster is a fast and flexible program for marking duplicates in read-id sorted paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file.
When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.
Environment Modules
Run module spider samblaster to find out what environment modules are available for this application.
System Variables
- HPC_SAMBLASTER_DIR - installation directory
- HPC_SAMBLASTER_DIR - executable directory