TopHat-Recondition: A post-processor for TopHat unmapped reads

Research output: Contribution to journalArticlepeer-review


Background: TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format - the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for aligned sequencing reads, thus correct format implementation is paramount for software interoperability and correct analysis. However, TopHat writes its unmapped reads in a way that is not compatible with other software that implements the SAM/BAM format. Results: We have developed TopHat-Recondition, a post-processor for TopHat unmapped reads that restores read information in the proper format. TopHat-Recondition thus enables downstream software to process the plethora of BAM files written by TopHat. Conclusions: TopHat-Recondition can repair unmapped read files written by TopHat and is freely available under a 2-clause BSD license on GitHub:

Original languageEnglish
Article number199
JournalBMC Bioinformatics
Issue number1
Publication statusPublished - 2016 May 4

Subject classification (UKÄ)

  • Basic Medicine

Free keywords

  • Deep sequencing
  • RNA-seq
  • Sequence alignment
  • Sequence analysis


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