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Accurate assembly of transcripts through phase-preserving graph decomposition


We introduce Scallop, an accurate reference-based transcript assembler that improves reconstruction of multi-exon and lowly expressed transcripts. Scallop preserves long-range phasing paths extracted from reads, while producing a parsimonious set of transcripts and minimizing coverage deviation. On 10 human RNA-seq samples, Scallop produces 34.5% and 36.3% more correct multi-exon transcripts than StringTie and TransComb, and respectively identifies 67.5% and 52.3% more lowly expressed transcripts. Scallop achieves higher sensitivity and precision than previous approaches over a wide range of coverage thresholds.

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Figure 1: Comparison of the three methods (StringTie, TransComb, and Scallop) over the five testing samples.
Figure 2: Overview of Scallop.


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We thank Cong Ma and Juntao Liu for helpful suggestions and discussions. This research is funded in part by the Gordon and Betty Moore Foundation's Data-Driven Discovery Initiative through Grant GBMF4554 to C.K., by The Shurl and Kay Curci Foundation, by the US National Science Foundation (CCF-1256087, CCF-1319998), and by the US National Institutes of Health (R01HG007104 and R01GM122935).

Author information




M.S. and C.K. designed the method, and M.S. implemented it. M.S. and C.K. designed the experiments, and M.S. conducted them. M.S. and C.K. wrote the manuscript.

Corresponding author

Correspondence to Carl Kingsford.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–21, Supplementary Tables 1–3, Supplementary Notes 1–7 (PDF 2473 kb)

Life Sciences Reporting Summary (PDF 176 kb)

Supplementary Code

Source Code of Scallop (ZIP 178 kb)

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Shao, M., Kingsford, C. Accurate assembly of transcripts through phase-preserving graph decomposition. Nat Biotechnol 35, 1167–1169 (2017).

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