accurate assembly of transcripts through phase-preserving graph decomposition

Mingfu Shao, Carl Kingsford

Research output: Contribution to journalArticle

19 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1167-1169
Number of pages3
JournalNature Biotechnology
Volume35
Issue number12
DOIs
StatePublished - Jan 1 2017

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All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering

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