RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition

Publishing date: 2020-08-18

Published on: PLOS ONE

summary: High throughput RNA-Seq has become a staple in modern molecular biology, with applications not only in quantifying gene expression but also in isoform-level analysis of the RNA transcripts. To enable such an isoform-level analysis, a transcriptome assembly algorithm is utilized to stitch together the observed short reads into the corresponding transcripts. This task is complicated due to the complexity of alternative splicing - a mechanism by which the same gene may generate multiple distinct RNA transcripts. Mao et al develop a novel genome-guided transcriptome assembler, RefShannon, that exploits the varying abundances of the different transcripts, in enabling an accurate reconstruction of the transcripts.

authors: Shunfu Mao, Lior Pachter, David Tse, Sreeram Kannan

link to paper: 10.1371/journal.pone.0232946

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