General Information
| Description | Evaluating next-generation sequencing alignment data |
| Homepage | http://www.qualimap.org |
Publications
Qualimap: evaluating next-generation sequencing alignment data
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 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.
Contact:
aconesa@cipf.es
Supplementary Information:
Supplementary data are available at Bioinformatics online.
Related Tools
The GNUMAP algorithm
Published October 2009
Unbiased probabilistic mapping of oligonucleotides from next-generation sequencing
BamView
Published January 2010
Viewing mapped read alignment data in the context of the reference sequence
ngsTools
Published January 2014
Methods for population genetics analyses from next-generation sequencing data
Qualimap 2
Published October 2015
Advanced multi-sample quality control for high-throughput sequencing data
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