Difference between revisions of "Scythe"

From UFRC
Jump to navigation Jump to search
(Created page with "Category:SoftwareCategory:BioinformaticsCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|scythe}} |{{#vardefine:url|https://github.com/vsbuffalo/scy...")
 
 
(3 intermediate revisions by 3 users not shown)
Line 1: Line 1:
[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+
[[Category:Software]][[Category:Biology]][[Category:NGS]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|scythe}}
 
|{{#vardefine:app|scythe}}
Line 21: Line 21:
  
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
===Serial===
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 20:36, 12 August 2022

Description

scythe website  

Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases.

Environment Modules

Run module spider scythe to find out what environment modules are available for this application.

System Variables

  • HPC_SCYTHE_DIR - installation directory