RNA-Skim 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 Cited in: 1 Publication Cited by 3 Authors 1 Pellegrina, Leonardo 1 Pizzi, Cinzia 1 Vandin, Fabio Cited in 0 Serials Cited in 1 Field 1 Biology and other natural sciences (92-XX) Citations by Year