TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

dc.contributor.authorKim, Daehwan
dc.contributor.authorPertea, Geo
dc.contributor.authorTrapnell, Cole
dc.contributor.authorPimentel, Harold
dc.contributor.authorKelley, Ryan
dc.contributor.authorSalzberg, Steven L
dc.date.accessioned2021-09-28T14:05:30Z
dc.date.available2021-09-28T14:05:30Z
dc.date.issued2013-04-25
dc.description.abstractTopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. In addition to de novo spliced alignment, TopHat2 can align reads across fusion breaks, which can occur after genomic translocations. TopHat2 combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. TopHat2 is available at http://ccb.jhu.edu/software/tophat .en_US
dc.description.urihttps://doi.org/10.1186/gb-2013-14-4-r36
dc.identifierhttps://doi.org/10.13016/7jyb-2sdy
dc.identifier.citationKim, D., Pertea, G., Trapnell, C. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14, R36 (2013).en_US
dc.identifier.urihttp://hdl.handle.net/1903/28030
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCollege of Computer, Mathematical & Natural Sciencesen_us
dc.relation.isAvailableAtComputer Scienceen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectSplice Siteen_US
dc.subjectEdit Distanceen_US
dc.subjectEntire Human Genomeen_US
dc.subjectMultiple Exonen_US
dc.subjectTranscriptome Mappingen_US
dc.titleTopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusionsen_US
dc.typeArticleen_US

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