Monday 27 August 2012

Qualimap: evaluating next generation sequencing alignment data.

http://www.ncbi.nlm.nih.gov/pubmed/22914218
Bioinformatics. 2012 Aug 22. [Epub ahead of print]

Qualimap: evaluating next generation sequencing alignment data.

Source

Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain.

Abstract

MOTIVATION:

The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of representation 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 technology, 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 to drive appropriate downstream analyses.

RESULTS:

We have developed Qualimap, a Java application that supports user-friendly quality control of mapping data, by considering sequence features and their genomic properties. Qualimap takes sequence alignment data and provides graphical and statistical analyses for the evaluation of data. Such quality-control data are vital for highlighting problems in the sequencing and/or mapping processes, which must be addressed prior to further analyses.

AVAILABILITY:

Qualimap is freely available from http://www.qualimap.org


http://qualimap.bioinfo.cipf.es/samples/ERR089819_result/qualimapReport.html


Coverage across reference

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