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

Daehwan Kim123*, Geo Pertea3, Cole Trapnell56, Harold Pimentel7, Ryan Kelley8 and Steven L Salzberg34

Author Affiliations

1 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA

2 Department of Computer Science, University of Maryland, College Park, MD 20742, USA

3 Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA

4 Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD, 21205, USA

5 Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA

6 Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA, 02142, USA

7 Department of Electrical Engineering and Computer Science, University of California, 101 Sproul Hall, Berkeley, CA, 94720, USA

8 Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA

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Genome Biology 2013, 14:R36  doi:10.1186/gb-2013-14-4-r36

Published: 25 April 2013

Additional files

Additional File 1:

Supplementary material.

Format: DOCX Size: 209KB Download file

Open Data

Additional File 2:

TopHat2 source code.

Format: GZ Size: 1.7MB Download file

Open Data