Difference between revisions of "QualiMap"

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(Created page with "Category:SoftwareCategory:BiologyCategory:Sequence Alignment {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|qualimap}} |{{#vardefine:url|http://qualimap.bioinf...")
 
 
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[[Category:Software]][[Category:Biology]][[Category:Sequence Alignment]]
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[[Category:Software]][[Category:Biology]][[Category:Alignment‏]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|qualimap}}
 
|{{#vardefine:app|qualimap}}
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
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|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
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<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
 
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
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{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
  
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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Available tools:
 +
 
 +
*bamqc - Evaluate NGS mapping to a reference genome
 +
*rnaseq - Evaluate RNA-seq alignment data
 +
*counts - Counts data analysis (further RNA-seq data evaluation)
 +
*multi-bamqc - Compare QC reports from multiple NGS mappings
 +
*clustering - Cluster epigenomic signals
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*comp-counts - Compute feature counts
  
 
|}}
 
|}}

Latest revision as of 19:32, 24 August 2022

Description

qualimap website  

Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

Environment Modules

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

System Variables

  • HPC_QUALIMAP_DIR - installation directory

Additional Information

Available tools:

  • bamqc - Evaluate NGS mapping to a reference genome
  • rnaseq - Evaluate RNA-seq alignment data
  • counts - Counts data analysis (further RNA-seq data evaluation)
  • multi-bamqc - Compare QC reports from multiple NGS mappings
  • clustering - Cluster epigenomic signals
  • comp-counts - Compute feature counts



Citation

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

Konstantin Okonechnikov, Ana Conesa and Fernando García-Alcalde "Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data." Bioinformatics(2015)