Difference between revisions of "Stampy"
Jump to navigation
Jump to search
(Created page with "Category:SoftwareCategory:BiologyCategory:BioinformaticsCategory:Sequencing {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|stampy}} |{{#vardefine:url|http:...") |
|||
| (2 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category:Biology | + | [[Category:Software]][[Category:Biology]][[Category:Sequencing]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|stampy}} | |{{#vardefine:app|stampy}} | ||
| Line 21: | Line 21: | ||
<!--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_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 20:45, 12 August 2022
Description
Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model.
Environment Modules
Run module spider stampy to find out what environment modules are available for this application.
System Variables
- HPC_STAMPY_DIR - installation directory
- HPC_STAMPY_BIN - executable directory