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...

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Vydáno v:Bioinformatics (Oxford, England) Ročník 28; číslo 20; s. 2678 - 2679
Hlavní autoři: García-Alcalde, Fernando, Okonechnikov, Konstantin, Carbonell, José, Cruz, Luis M., Götz, Stefan, Tarazona, Sonia, Dopazo, Joaquín, Meyer, Thomas F., Conesa, Ana
Médium: Journal Article
Jazyk:angličtina
Vydáno: Oxford Oxford University Press 15.10.2012
Témata:
Algorithms
Biological and medical sciences
Fundamental and applied biological sciences. Psychology
General aspects
Genomics
High-Throughput Nucleotide Sequencing
Humans
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Quality Control
Sequence Alignment - standards
Software
Sequencing
Data
ISSN:1367-4803, 1367-4811, 1367-4811
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Shrnutí: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.
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ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/bts503