Difference between revisions of "QUAST"

Latest revision as of 21:01, 21 August 2022

Description

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

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]][[Category:RNA-Seq]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|quast}}
@@ Line 25: / Line 25: @@
 <!--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==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==