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Genomics. 2010 Jun;95(6):315-27. doi: 10.1016/j.ygeno.2010.03.001. Epub 2010 Mar 6.

Assembly algorithms for next-generation sequencing data.

Author information

1
J. Craig Venter Institute, Rockville, MD 20850-3343, USA. jmiller@jcvi.org

Abstract

The emergence of next-generation sequencing platforms led to resurgence of research in whole-genome shotgun assembly algorithms and software. DNA sequencing data from the Roche 454, Illumina/Solexa, and ABI SOLiD platforms typically present shorter read lengths, higher coverage, and different error profiles compared with Sanger sequencing data. Since 2005, several assembly software packages have been created or revised specifically for de novo assembly of next-generation sequencing data. This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. More generally, it compares the two standard methods known as the de Bruijn graph approach and the overlap/layout/consensus approach to assembly.

PMID:
20211242
PMCID:
PMC2874646
DOI:
10.1016/j.ygeno.2010.03.001
[Indexed for MEDLINE]
Free PMC Article

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