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: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:GUI Apps]] |
{|<!--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--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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==System Variables== | ==System Variables== | ||
− | * HPC_{{ | + | * 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== | ||
− | + | 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 | ||
|}} | |}} |
Revision as of 21:24, 6 December 2019
Description
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.
Required Modules
Serial
- qualimap
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: