- -

Qualimap: evaluating next generation sequencing alignment data

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

Qualimap: evaluating next generation sequencing alignment data

Mostrar el registro sencillo del ítem

Ficheros en el ítem

Thumbnail
Nombre: García-Alcalde, F. ...
Tamaño: 156.7Kb
Formato: PDF
Descripción: Versión editorial
Abrir
dc.contributor.author García-Alcalde, Fernando es_ES
dc.contributor.author Okonechnikov, Konstantin es_ES
dc.contributor.author Carbonell Caballero, José es_ES
dc.contributor.author Cruz, Luís M. es_ES
dc.contributor.author GOTZ, STEFAN es_ES
dc.contributor.author Tarazona Campos, Sonia es_ES
dc.contributor.author Dopazo, Joaquín es_ES
dc.contributor.author Meyer, Thomas F. es_ES
dc.contributor.author Conesa, Ana es_ES
dc.date.accessioned 2014-05-19T11:28:54Z
dc.date.available 2014-05-19T11:28:54Z
dc.date.issued 2012
dc.identifier.issn 1367-4803
dc.identifier.uri http://hdl.handle.net/10251/37553
dc.description.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 ¿les 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 es_ES
dc.language Inglés es_ES
dc.publisher Oxford University Press (OUP): Policy B - Oxford Open Option B es_ES
dc.relation.ispartof Bioinformatics es_ES
dc.rights Reserva de todos los derechos es_ES
dc.subject.classification ESTADISTICA E INVESTIGACION OPERATIVA es_ES
dc.title Qualimap: evaluating next generation sequencing alignment data es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1093/bioinformatics/bts503
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Estadística e Investigación Operativa Aplicadas y Calidad - Departament d'Estadística i Investigació Operativa Aplicades i Qualitat es_ES
dc.contributor.affiliation Universitat Politècnica de València. Facultad de Informática - Facultat d'Informàtica es_ES
dc.description.bibliographicCitation García-Alcalde, F.; Okonechnikov, K.; Carbonell Caballero, J.; Cruz, LM.; Gotz, S.; Tarazona Campos, S.; Dopazo, J.... (2012). Qualimap: evaluating next generation sequencing alignment data. Bioinformatics. 28(20):2678-2679. doi:10.1093/bioinformatics/bts503 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://bioinformatics.oxfordjournals.org/content/28/20/2678.full es_ES
dc.description.upvformatpinicio 2678 es_ES
dc.description.upvformatpfin 2679 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 28 es_ES
dc.description.issue 20 es_ES
dc.relation.senia 236919
dc.description.references DeLuca, D. S., Levin, J. Z., Sivachenko, A., Fennell, T., Nazaire, M.-D., Williams, C., … Getz, G. (2012). RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics, 28(11), 1530-1532. doi:10.1093/bioinformatics/bts196 es_ES
dc.description.references Flicek, P., & Birney, E. (2009). Sense from sequence reads: methods for alignment and assembly. Nature Methods, 6(S11), S6-S12. doi:10.1038/nmeth.1376 es_ES
dc.description.references Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Chen, Y., … Fitzgerald, S. (2010). Ensembl 2011. Nucleic Acids Research, 39(Database), D800-D806. doi:10.1093/nar/gkq1064 es_ES
dc.description.references Harismendy, O., Ng, P. C., Strausberg, R. L., Wang, X., Stockwell, T. B., Beeson, K. Y., … Frazer, K. A. (2009). Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biology, 10(3), R32. doi:10.1186/gb-2009-10-3-r32 es_ES
dc.description.references Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10(3), R25. doi:10.1186/gb-2009-10-3-r25 es_ES
dc.description.references Lassmann, T., Hayashizaki, Y., & Daub, C. O. (2010). SAMStat: monitoring biases in next generation sequencing data. Bioinformatics, 27(1), 130-131. doi:10.1093/bioinformatics/btq614 es_ES
dc.description.references Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., … Homer, N. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:10.1093/bioinformatics/btp352 es_ES
dc.description.references Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., & Gilad, Y. (2008). RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Research, 18(9), 1509-1517. doi:10.1101/gr.079558.108 es_ES
dc.description.references Metzker, M. L. (2009). Sequencing technologies — the next generation. Nature Reviews Genetics, 11(1), 31-46. doi:10.1038/nrg2626 es_ES
dc.description.references Statham, A. L., Strbenac, D., Coolen, M. W., Stirzaker, C., Clark, S. J., & Robinson, M. D. (2010). Repitools: an R package for the analysis of enrichment-based epigenomic data. Bioinformatics, 26(13), 1662-1663. doi:10.1093/bioinformatics/btq247 es_ES
dc.description.references Trapnell, C., & Salzberg, S. L. (2009). How to map billions of short reads onto genomes. Nature Biotechnology, 27(5), 455-457. doi:10.1038/nbt0509-455 es_ES
dc.description.references Trapnell, C., Pachter, L., & Salzberg, S. L. (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25(9), 1105-1111. doi:10.1093/bioinformatics/btp120 es_ES


Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro sencillo del ítem