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Scallop enables accurate assembly of transcripts through phasing-preserving graph decomposition

Mingfu Shao, Carl Kingsford
doi: https://doi.org/10.1101/123612
Mingfu Shao
1Computational Biology Department, School of Computer Science, Carnegie Mellon University
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  • For correspondence: mingfu.shao@cs.cmu.edu
Carl Kingsford
1Computational Biology Department, School of Computer Science, Carnegie Mellon University
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  • For correspondence: carlk@cs.cmu.edu
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Abstract

We introduce Scallop, an accurate, reference-based transcript assembler for RNA-seq data. Scallop significantly improves reconstruction of multi-exon and lowly expressed transcripts. On 10 human samples aligned with STAR, Scallop produces (on average) 35.7% and 37.5% more correct multi-exon transcripts than two leading transcript assemblers, StringTie [1] and TransComb [2], respectively. For transcripts expressed at low levels in the same samples, Scallop assembles 65.2% and 50.2% more correct multi-exon transcripts than StringTie and TransComb, respectively. Scallop obtains this improvement through a novel algorithm that we prove preserves all phasing paths from reads (including paired-end reads), while also producing a parsimonious set of transcripts and minimizing coverage deviation.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 03, 2017.
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Scallop enables accurate assembly of transcripts through phasing-preserving graph decomposition
Mingfu Shao, Carl Kingsford
bioRxiv 123612; doi: https://doi.org/10.1101/123612
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Scallop enables accurate assembly of transcripts through phasing-preserving graph decomposition
Mingfu Shao, Carl Kingsford
bioRxiv 123612; doi: https://doi.org/10.1101/123612

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