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. 2018 Oct 4;19(1):153.
doi: 10.1186/s13059-018-1540-z.

SKESA: strategic k-mer extension for scrupulous assemblies

Alexandre Souvorov  1 , Richa Agarwala  2 , David J Lipman  1   3
Affiliations

SKESA: strategic k-mer extension for scrupulous assemblies

Alexandre Souvorov et al. Genome Biol. .

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 https://github.com/ncbi/SKESA/releases .

Keywords: Contamination; De-novo assembly; DeBruijn graphs; Illumina reads; Sequence quality.

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Competing interests

Authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
Substrings mismatches: mismatches per 100 Kb seen in assemblies of SPAdes and MegaHit for inputs in substrings set. SKESA has no mismatches at any length in this set
Fig. 2
Fig. 2
Substrings contiguity: N50 for assemblies generated by SKESA, SPAdes, and MegaHit for inputs in substrings set
Fig. 3
Fig. 3
Substrings deviation: deviation for assemblies generated by SKESA, SPAdes, and MegaHit for inputs in substrings set. We do not show values for input length 22 where MegaHit has value of almost 100 and input length 34 and 56 for which SPAdes did not produce an assembly
Fig. 4
Fig. 4
SKESA flowchart: flowchart describing main steps in the algorithm used by SKESA for assembly
Fig. 5
Fig. 5
Main distribution in SRR2821438: histogram for frequency of 21-mers seen in SRR2821438 with counts on X axis up to 400 and number of 21-mers with that count on Y axis
Fig. 6
Fig. 6
Small distributions in SRR2821438: histogram for frequency of 21-mers seen in SRR2821438 with counts on X axis between 325 and 2000 and number of 21-mers with that count on Y axis
See this image and copyright information in PMC

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