Accurate assembly of transcripts through phase-preserving graph decomposition.
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ABSTRACT:
SUBMITTER: Shao M
PROVIDER: S-EPMC5722698 | biostudies-literature | 2017 Dec
REPOSITORIES: biostudies-literature
Publications
Accurate assembly of transcripts through phase-preserving graph decomposition.
Shao Mingfu M Kingsford Carl C
Nature biotechnology 20171113 12
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 transcript ...[more]
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