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Genome Res DOI:10.1101/gr.7337908

ALLPATHS: de novo assembly of whole-genome shotgun microreads.

Publication TypeJournal Article
Year of Publication2008
AuthorsButler, J, MacCallum, I, Kleber, M, Shlyakhter, IA, Belmonte, MK, Lander, ES, Nusbaum, C, Jaffe, DB
JournalGenome Res
Date Published2008 May
KeywordsAlgorithms, Campylobacter jejuni, Computational Biology, Computer Simulation, Escherichia coli, Genome, Bacterial, Reproducibility of Results, Sequence Analysis, DNA

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 80x 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.


Alternate JournalGenome Res.
PubMed ID18340039
PubMed Central IDPMC2336810
Grant ListR01 HG003474 / HG / NHGRI NIH HHS / United States
5R01HG003474 / HG / NHGRI NIH HHS / United States