swMATH ID: 36880
Software Authors: Melsted, P., Halldórsson, B.V.
Description: KmerStream: streaming algorithms for k-mer abundance estimation. Results: We present KmerStream, a streaming algorithm for estimating the number of distinct k -mers present in high-throughput sequencing data. The algorithm runs in time linear in the size of the input and the space requirement are logarithmic in the size of the input. We derive a simple model that allows us to estimate the error rate of the sequencing experiment, as well as the genome size, using only the aggregate statistics reported by KmerStream. As an application we show how KmerStream can be used to compute the error rate of a DNA sequencing experiment. We run KmerStream on a set of 2656 whole genome sequenced individuals and compare the error rate to quality values reported by the sequencing equipment. We discover that while the quality values alone are largely reliable as a predictor of error rate, there is considerable variability in the error rates between sequencing runs, even when accounting for reported quality values. Availability and implementation: The tool KmerStream is written in C++ and is released under a GPL license. It is freely available at https://github.com/pmelsted/KmerStream
Homepage: https://academic.oup.com/bioinformatics/article/30/24/3541/2422237
Source Code:  https://github.com/pmelsted/KmerStream
Dependencies: C++
Related Software: Quake; Salmon; LBFGS-B; L-BFGS; L-BFGS-B; MetaProb; SAKEIMA; ntCard; RNA-Skim; Kraken; Kmerlight; Squeakr; Turtle; KMC; Velvet
Cited in: 2 Documents

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