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
- Strawberry
- Liu, R., & Dickerson, J. (2017). Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq. PLoS Computational Biology, 13(11), e1005851–25
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