TopHat 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.
%0 Journal Article
%1 Kim2013TopHat2accuratealignment
%A Kim, Daehwan
%A Pertea, Geo
%A Trapnell, Cole
%A Pimentel, Harold
%A Kelley, Ryan
%A Salzberg, Steven L
%D 2013
%J Genome Biol
%K imported
%N 4
%P R36
%R 10.1186/gb-2013-14-4-r36
%T TopHat2: accurate alignment of transcriptomes in the presence of
insertions, deletions and gene fusions.
%U http://dx.doi.org/10.1186/gb-2013-14-4-r36
%V 14
%X TopHat 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.
@article{Kim2013TopHat2accuratealignment,
abstract = {TopHat 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.},
added-at = {2014-05-13T15:48:44.000+0200},
author = {Kim, Daehwan and Pertea, Geo and Trapnell, Cole and Pimentel, Harold and Kelley, Ryan and Salzberg, Steven L},
biburl = {https://www.bibsonomy.org/bibtex/2b00202d1e4c925691507ec26e5988d6c/gwotto},
doi = {10.1186/gb-2013-14-4-r36},
file = {:Kim2013TopHat2accuratealignment.pdf:PDF},
institution = {Center for Bioinformatics and Computational Biology{\,} University
of Maryland{\,} College Park{\,} MD{\,} 20742{\,} USA. infphilo@umiacs.umd.edu.},
interhash = {db9a8472bcd951f565a24b03f5af3d7c},
intrahash = {b00202d1e4c925691507ec26e5988d6c},
journal = {Genome Biol},
keywords = {imported},
language = {eng},
medline-pst = {aheadofprint},
month = Apr,
number = 4,
owner = {gotto},
pages = {R36},
pii = {gb-2013-14-4-r36},
pmid = {23618408},
timestamp = {2014-05-13T15:48:44.000+0200},
title = {TopHat2: accurate alignment of transcriptomes in the presence of
insertions, deletions and gene fusions.},
url = {http://dx.doi.org/10.1186/gb-2013-14-4-r36},
volume = 14,
year = 2013
}