ALLPATHS: de novo assembly of whole-genome shotgun microreads

Butler, J., MacCallum, I., Kleber, M., Shlyakhter, I.A., Belmonte, M.K. ORCID: 0000-0002-4633-9400, Lander, E.S., Nusbaum, C. and Jaffe, D.B., 2008. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Research, 18 (5), pp. 810-820. ISSN 1088-9051

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Abstract

New DNA sequencing technologies deliver data at dramatically lower costs but demand new analytical methods to take full advantage of the very short reads that they produce. We provide an initial, theoretical solution to the challenge of de novo assembly from whole-genome shotgun “microreads.” For 11 genomes of sizes up to 39 Mb, we generated high-quality assemblies from 80× coverage by paired 30-base simulated reads modeled after real Illumina-Solexa reads. The bacterial genomes of Campylobacter jejuni and Escherichia coli assemble optimally, yielding single perfect contigs, and larger genomes yield assemblies that are highly connected and accurate. Assemblies are presented in a graph form that retains intrinsic ambiguities such as those arising from polymorphism, thereby providing information that has been absent from previous genome assemblies. For both C. jejuni and E. coli, this assembly graph is a single edge encompassing the entire genome. Larger genomes produce more complicated graphs, but the vast majority of the bases in their assemblies are present in long edges that are nearly always perfect. We describe a general method for genome assembly that can be applied to all types of DNA sequence data, not only short read data, but also conventional sequence reads.

Item Type: Journal article
Publication Title: Genome Research
Creators: Butler, J., MacCallum, I., Kleber, M., Shlyakhter, I.A., Belmonte, M.K., Lander, E.S., Nusbaum, C. and Jaffe, D.B.
Publisher: Cold Spring Harbor Laboratory Press
Place of Publication: Cold Spring Harbor, NY
Date: 2008
Volume: 18
Number: 5
ISSN: 1088-9051
Identifiers:
NumberType
10.1101/gr.7337908DOI
Rights: Copyright © 2008, Cold Spring Harbor Laboratory Press
Divisions: Schools > School of Social Sciences
Depositing User: EPrints Services
Date Added: 09 Oct 2015 11:11
Last Modified: 09 Jun 2017 13:52
URI: http://irep.ntu.ac.uk/id/eprint/24156

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