ALLPATHS 2: Small Genomes Assembled Accurately and with High Continuity from Short Paired Reads

 
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MacCallum, Iain
Przybylski, Dariusz
Gnerre, Sante
Burton, Joshua
Gnirke, Andreas
Malek, Joel
McKernan, Kevin
Ranade, Swati
Shea, Terrance P
Williams, Louise
Nusbaum, Chad
Jaffe, David B
Young, Sarah
Note: Order does not necessarily reflect citation order of authors.
Published Version
https://doi.org/10.1186/gb-2009-10-10-r103
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Citation
MacCallum, Iain, Dariusz Przybylski, Sante Gnerre, Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, et al. 2009. ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biology 10:R103.
Abstract
We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds. Velvet and EULER-SR were less accurate. For example, for Escherichia coli, the fraction of 10-kb stretches that were perfect was 99.8% (ALLPATHS2), 68.7% (Velvet), and 42.1% (EULER-SR).
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784318/pdf/
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This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
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http://nrs.harvard.edu/urn-3:HUL.InstRepos:4551386

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