Softwares

  • Scallop is an accurate reference-based transcriptome assembler. Software is available at github. Scallop has been published at Nature Biotechnology. A podcast about Scallop (thanks to Roman Cheplyaka for the interview) is available at both bioinformatics.chat and iTunes.
  • Scallop-LR is a reference-based transcriptome assembler for PacBio Iso-Seq data. Software is available at github. Manuscript for this work is under preparation.
  • DeepBound presents a new framework to identify boundaries of expressed transcripts from RNA-seq alignments using convolutional neural networks. Software is available at github. DeepBound has been published at Bioinformatics.
  • Coral is an efficient tool to determine the alignments in splice graph of the unsequenced portion for paired-end reads. Software is available at github. Manuscript for this work is under preparation.
  • Catfish implements an efficient algorithm for the flow decomposition problem, the abstracted mathematical formulation for transcript assembly. Software is available at github. Catfish has been published at IEEE/ACM Transactions on Computational Biology and Bioinformatics.
  • SQUID presents an algorithm to identity transcriptomic structural variations from RNA-seq alignments. Software is available at github. SQUID has been published at Genome Biology.
  • GREDU (Genome REarrangements with DUplications) is a software package that implements fast and exact algorithms for the following five edit distance problems between pairwise genomes with duplicate genes:
    1. DCJ distance
    2. DCJ + segmental duplication distance
    3. exemplar breakpoint distance
    4. intermediate breakpoint distance
    5. maximum-matching breakpoint distance

    Released source code is at github. Reference manual is here.