QualiMap

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.

Required Modules

Serial

• qualimap

System Variables

• HPC_{{#uppercase: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)