Genome analysis Advance Access publication August 22, 2012 Qualimap: evaluating next-generation sequencing alignment data

Motivation: The sequence alignment/map (SAM) and the binary align-ment/map (BAM) formats have become the standard method of rep-resentation of nucleotide sequence alignments for next-generation sequencing data. SAM/BAM files usually contain information from tens to hundreds of millions of reads. Often, the sequencing technol-ogy, protocol and/or the selected mapping algorithm introduce some unwanted biases in these data. The systematic detection of such biases is a non-trivial task that is crucial to drive appropriate down-stream analyses. Results: We have developed Qualimap, a Java application that sup-ports user-friendly quality control of mapping data, by considering sequence features and their genomic properties. Qualimap takes se-quence alignment data and provides graphical and statistical analyses for the evaluation of data. Such quality-control data are vital for high-lighting problems in the sequencing and/or mapping processes, which must be addressed prior to further analyses