Difference between revisions of "QUAST"

From UFRC
Jump to navigation Jump to search
 
(3 intermediate revisions by 2 users not shown)
Line 1: Line 1:
[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]][[Category:RNA-Seq]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|quast}}
 
|{{#vardefine:app|quast}}
Line 25: Line 25:
  
 
<!--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.
* gcc/5.2.0
 
* {{#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 21:01, 21 August 2022

Description

quast website  

QUAST performs fast and convenient quality evaluation and comparison of genome assemblies.

QUAST computes a number of well-known metrics, including contig accuracy, number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper andin the manual). A comprehensive analysis results in summary tables (in plain text, tab-separated and LaTeX formats) and colorful plots. The tool also produces web-based reports condensing all information in one easy to navigate file.

QUAST has an intuitive command-line interface and a detailed manual to help users run it and understand its output.

Environment Modules

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

System Variables

  • HPC_QUAST_DIR - installation directory




Citation

If you publish research that uses quast you have to cite it as follows:

QUAST paper is available at Bioinformatics Advance Access http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btt086?ijkey=Kzq9lhMayiqecq9&keytype=ref