SKESA: strategic k-mer extension for scrupulous assemblies

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, an...

Descripción completa

Detalles Bibliográficos
Autores principales: Souvorov, Alexandre, Agarwala, Richa, Lipman, David J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172800/
https://www.ncbi.nlm.nih.gov/pubmed/30286803
http://dx.doi.org/10.1186/s13059-018-1540-z
_version_ 1783361012684029952
author Souvorov, Alexandre
Agarwala, Richa
Lipman, David J.
author_facet Souvorov, Alexandre
Agarwala, Richa
Lipman, David J.
author_sort Souvorov, Alexandre
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1540-z) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-6172800
institution National Center for Biotechnology Information
language English
publishDate 2018
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-61728002018-10-15 SKESA: strategic k-mer extension for scrupulous assemblies Souvorov, Alexandre Agarwala, Richa Lipman, David J. Genome Biol Software 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1540-z) contains supplementary material, which is available to authorized users. BioMed Central 2018-10-04 /pmc/articles/PMC6172800/ /pubmed/30286803 http://dx.doi.org/10.1186/s13059-018-1540-z Text en © The Author(s) 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Souvorov, Alexandre
Agarwala, Richa
Lipman, David J.
SKESA: strategic k-mer extension for scrupulous assemblies
title SKESA: strategic k-mer extension for scrupulous assemblies
title_full SKESA: strategic k-mer extension for scrupulous assemblies
title_fullStr SKESA: strategic k-mer extension for scrupulous assemblies
title_full_unstemmed SKESA: strategic k-mer extension for scrupulous assemblies
title_short SKESA: strategic k-mer extension for scrupulous assemblies
title_sort skesa: strategic k-mer extension for scrupulous assemblies
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172800/
https://www.ncbi.nlm.nih.gov/pubmed/30286803
http://dx.doi.org/10.1186/s13059-018-1540-z
work_keys_str_mv AT souvorovalexandre skesastrategickmerextensionforscrupulousassemblies
AT agarwalaricha skesastrategickmerextensionforscrupulousassemblies
AT lipmandavidj skesastrategickmerextensionforscrupulousassemblies

Ejemplares similares