Qualimap: evaluating next generation sequencing alignment data
Qualimap is a platform-independent application written in Java and R that provides both a GraphicalUser Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.
Qualimap examines sequencing alignment data inSAM/BAM files according to the features of themapped reads and provides an overall view of thedata that helps to the detect biases in the sequencingand/or mapping of the data and eases decision-making for further analysis.
- Fast analysis accross the reference of genomecoverage and nucleotide distribution;
- Easy to interpret summary of the main properties of the alignment data;
- Analysis of the reads mapped inside/outside of the regions provided in GFF format;
- Insert size mean and median value calculation and plotting statistical distribution;
- Analysis of the adequasy of the sequencing depth in RNA-seq experiments;
- Clustering of epigenomic profiles.
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