Introduction

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.

Publications

  1. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
    Cite this
    Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL, 2013-04-01 - Genome biology

Credits

  1. Daehwan Kim
    Developer

  2. Geo Pertea
    Developer

  3. Cole Trapnell
    Developer

  4. Harold Pimentel
    Developer

  5. Ryan Kelley
    Developer

  6. Steven L Salzberg
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006187
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted BySteven L Salzberg