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SKESA: strategic k-mer extension for scrupulous assemblies

Genome Biology. 2018;19(1):1-13 DOI 10.1186/s13059-018-1540-z


Journal Homepage

Journal Title: Genome Biology

ISSN: 1474-760X (Online)

Publisher: BMC

LCC Subject Category: Science: Biology (General): Genetics

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML



Alexandre Souvorov (NCBI/NLM/NIH/DHHS)

Richa Agarwala (NCBI/NLM/NIH/DHHS)

David J. Lipman (NCBI/NLM/NIH/DHHS)


Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 14 weeks


Abstract | Full Text

Abstract SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity, handles low-level contamination in reads, is fast, and produces an identical assembly for the same input when assembled multiple times with the same or different compute resources. SKESA has been used for assembling over 272,000 read sets in the Sequence Read Archive at NCBI and for real-time pathogen detection. Source code for SKESA is freely available at