cole AT broadinstitute dot org

7 Cambridge Center / 60747-A
Cambridge, MA, 02142


TopHat: RNA-Seq read alignment

TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify known and novel splice junctions between exons.

TopHat is a collaborative effort between the University of Maryland Center for Bioinformatics and Computational Biology and the University of California, Berkeley Departments of Mathematics and Molecular and Cell Biology.

Cufflinks: transcriptome assembly and differential expression analysis

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

Cufflinks is a collaborative effort between the Laboratory for Mathematical and Computational Biology, led by Lior Pachter at UC Berkeley, Steven Salzberg's group at the University of Maryland Center for Bioinformatics and Computational Biology, and Barbara Wold's lab at Caltech.

Bowtie: ultrafast short read alignment

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

Bowtie was primarily developed by Ben Langmead, with some help from me, at the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park.

MUMmerGPU: GPU-accelerated sequence alignment

MUMmerGPU is an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs) in common workstations. MUMmerGPU uses the Compute Unified Device Architecture (CUDA) from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree.

MUMmerGPU was developed by Michael Schatz and I at the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park.


  1. Stefanie A Mortimer, Cole Trapnell*, Sharon Aviran*, Lior Pachter, Julius B Lucks, "SHAPE–Seq: High‐Throughput RNA Structure Analysis", Current Protocols in Chemical Biology, 2013 [view]

  2. Lei Sun*, Loyal A Goff*, Cole Trapnell*, Ryan Alexander, Kinyui Alice Lo, Ezgi Hacisuleyman, Martin Sauvageau, Barbara Tazon-Vega, David R Kelley, David G Hendrickson, Bingbing Yuan, Manolis Kellis, Harvey F Lodish, John L Rinn, "Long noncoding RNAs regulate adipogenesis", PNAS, 2013 [view]

  3. Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R Kelley, Harold Pimentel, Steven L Salzberg, John L Rinn, Lior Pachter, "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks", Nature Protocols, 2012 [view]

  4. Cole Trapnell*, David Hendrickson*, Martin Sauvageau, Loyal Goff, John Rinn, Lior Pachter, "Differential analysis of gene regulation at transcript resolution with RNA-seq", Nature Biotechnology, 2012 [view]

  5. Tim R Mercer, Daniel J Gerhardt, Marcel E Dinger, Joanna Crawford, Cole Trapnell, Jeffrey A Jeddeloh, John S Mattick, John L Rinn, "Targeted RNA sequencing reveals the deep complexity of the human transcriptome", Nature Biotechnology, 2012 [view]

  6. Adam J Bogdanove et al., "Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp", Journal of Bacteriology, 2011 [view]

  7. Moran N. Cabili, Cole Trapnell, Loyal Goff, Magdalena Koziol, Barbara Tazon-Vega, Aviv Regev and John L. Rinn, "Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses", Genes and Development, 2011 [view]

  8. Adam Roberts, Harold Pimentel, Cole Trapnell*, and Lior Pachter*, "Identification of novel transcripts in annotated genomes using RNA-Seq", Bioinformatics, 2011 [view]

  9. Julius B. Lucks, Stefanie A. Mortimer, Cole Trapnell, Shujun Luo, Sharon Aviron, Lior Pachter, Jennifer A. Doudna, and Adam P. Arkin, "SHAPE-Seq: Multiplexed RNA Secondary and Tertiary Structure Determination." PNAS, 2011 [view]

  10. Sharon Aviran, Cole Trapnell, Julius B. Lucks, Stefanie A. Mortimer, Jennifer A. Doudna, Adam P. Arkin, and Lior Pachter, "Modeling and automation of SHAPE-Seq analysis." PNAS, 2011 [view]

  11. Manuel Garber, Manfred Grabherr, Mitchell Guttman and Cole Trapnell. "Computational methods for transcriptome annotation and quantification using RNA-seq." Nature Methods 8, 469–477 (2011). [view]

  12. Adam Roberts, Cole Trapnell, Julie Donaghey, John L. Rinn, and Lior Pachter, "Improving RNA-Seq expression estimates by correcting for fragment bias". Genome Biology 12:R22 (2011)

  13. Cole Trapnell, Brian A. Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J. van Baren, Steven L. Salzberg, Barbara J. Wold, and Lior Pachter. "Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms." Nature Biotechnology, 28, 511–515, doi:10.1038/nbt.1621 (2010) [view]

  14. Robert K. Bradley, Xiao-Yong Li, Cole Trapnell, Stuart Davidson, Lior Pachter, Hou Cheng Chu, Leath A. Tonkin, Mark D. Biggin, and Michael B. Eisen, "Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species." PLoS Biology, 8(3): e1000343. (2010) doi:10.1371/journal.pbio.1000343 [view]

  15. Cole Trapnell and Steven L. Salzberg, "How to map billions of short reads onto genomes." Nature Biotechnology, 27, 455 - 457 (2009) doi:10.1038/nbt0509-455 [view]

  16. Cole Trapnell, Lior Pachter, and Steven L. Salzberg, "TopHat: discovering splice junctions with RNA-Seq." Bioinformatics (2009), doi:10.1093/bioinformatics/btp120 [view]

  17. Ben Langmead, Cole Trapnell, Mihai Pop, and Steven L. Salzberg, "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome." Genome Biology, 10:R25 (2009) [view]

  18. Cole Trapnell* and Michael C. Schatz*, "Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment." Parallel Computing (2009), doi:10.1016/j.parco.2009.05.002 [view]

  19. Michael C. Schatz*, Cole Trapnell*, Arthur Delcher, and Amitabh Varshney, "High-throughput sequence alignment using Graphics Processing Units. BMC Bioinformatics 8:474 (2007) [view]

  20. Steven L. Salzberg et al., "Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A." BMC Genomics 9:204 (2008) [view]

  21. B. C. Trapnell, Jr., "A Peer-to-Peer Blacklisting Strategy Inspired by Leukocyte-Endothelium Interaction." In Proc. of the Fourth International Conference on Artificial Immune Systems, (ICARIS-05), Springer LNCS 3627, pages 339-352, 2005 [view]

  22. M. Neal, B. C. Trapnell, Jr., "Go Dutch: Exploiting Interactions in the Immune System." in In Silico Immunology, J Timmis and D Flower, 313-330, 2007 [view]