Reference-Based Transcript Identification

• Cufflinks
  • Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., et al. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 28(5), 516–520
• StringTie
  • Pertea, M., Pertea, G. M., Antonescu, C. M., Chang, T.-C., Mendell, J. T., & Salzberg, S. L. (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology, 33(3), 290–295
• TransComb
  • Liu, J., Yu, T., Jiang, T., & Li, G. (2016). TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs. Genome Biology, 17(1), 213
• Scallop
  • Shao, M., & Kingsford, C. (n.d.). Accurate assembly of transcripts through phase-preserving graph decomposition. Nature Biotechnology