swMATH ID: 36899
Software Authors: Zhaojun Zhang, Wei Wang
Description: RNA-Skim: a rapid method for RNA-Seq quantification at transcript level. Results: We propose a novel RNA-Seq quantification method, RNA-Skim, which partitions the transcriptome into disjoint transcript clusters based on sequence similarity, and introduces the notion of sig-mers, which are a special type of k-mers uniquely associated with each cluster. We demonstrate that the sig-mer counts within a cluster are sufficient for estimating transcript abundances with accuracy comparable with any state-of-the-art method. This enables RNA-Skim to perform transcript quantification on each cluster independently, reducing a complex optimization problem into smaller optimization tasks that can be run in parallel. As a result, RNA-Skim uses <4
Homepage: https://academic.oup.com/bioinformatics/article/30/12/i283/390499
Related Software: SAKEIMA; ntCard; Kraken; Kmerlight; Squeakr; KmerStream; MetaProb; Turtle; KMC; Velvet; Quake
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