An algorithm for Discovery of Novel Fusion Transcripts

TopHat-Fusion is an enhanced version of TopHat with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.

Open Source Software

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    New releases and related tools will be announced through the mailing list

Getting Help

    Questions about TopHat-Fusion should be sent to Please do not email technical questions to TopHat-Fusion contributors directly.

Related Tools

  • Cufflinks: Isoform assembly and quantitation for RNA-Seq
  • TopHat: A spliced read mapper for RNA-Seq
  • Bowtie: Ultrafast short read alignment




TopHat2 is released in which TopHat-Fusion is included (04/09/2012)

  • Now TopHat-Fusion engine is incorported into TopHat2 with the name of --fusion-search option, benefiting from TopHat2's advanced features.
  • Many bug fixes include some incompatibility issues with Python and memory problem in tophat_reports.
  • Annotations for Mouse, Rat, Dog, and Chicken are added. Please let us know if you need annotations for other genomes.
  • Fusion alignment format is slightly changed in a way compatible with SAM using optional fields "XF" and "XP" (see the output format for more detail)
  • In this version, you may want to use the older version of Bowtie (--bowtie1), which is much faster than with Bowtie2.

Important notes (12/19/2011)

  • If you have both TopHat and TopHat-Fusion installed on the same machine, you may need to put the path for TopHat-Fusion in your shell's PATH so that the sub-programs included in the TopHat-Fusion's package are used.
  • We have been working on the second version of TopHat-Fusion, which (we hope) will be available before March, 2012 in April, 2012.

Important notes (10/07/2011)

  • When installing TopHat-Fusion, if you already had TopHat (upon which TopHat-Fusion is based) installed somewhere, please make sure you install (or copy) all programs in TopHat-Fusion (tophat-fusion-0.1.0/bin) in a directory different than the one the binaries of TopHat are installed in. Otherwise, TopHat-Fusion will replace the binaries of TopHat with its own ones (, segment_juncs, or etc).
  • The current version of TopHat-Fusion has been tested using Python 2.7.1, so if you are using a different version of Python (2.6.X or 3.X), you are encouraged to try Python 2.7.1.

TopHat-Fusion paper published (8/11/2011)

The TopHat-Fusion paper has been published in Genome Biology.

TopHat-Fusion 0.1.0 (Beta) is released (5/09/2011)

The TopHat-Fusion algorithms are described in our poster at the CSHL Biology of Genomes conference.

  • We suggest that reads are at least 50-bp long, where a read is split into two segments (25-bp each) and at least two segments are required for identifying fusions. Shorter reads can be used if segment-length is set to a smaller value.
  • Both single and paired-end reads can be used and the output alignments are given in a modified SAM format where we added a new CIGAR* operator 'F' to indicate fusion points. (See Output for detailed information.)
    * CIGAR is an acronym for Concise Idiosyncratic Gapped Alignment Report.
  • This version does not support color-space reads although we have a plan to support it soon.
  • TopHat-Fusion consists of two sub-programs: tophat-fusion and tophat-fusion-post. For more information, please refer to Getting started.
  • This version is focused on identifying fusions due to chromosomal rearragements whether they are inter- or intra-chromosomal, but fusions due to read-through transcription or trans-splicing will be eventually supported. In addition to fusion read alignments, discordantly mapped pairs are output as well.
  • As an illustration, a sample output of TopHat-Fusion is given in HTML format. See Getting started.