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

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

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Title: ALLPATHS 2: Small Genomes Assembled Accurately and with High Continuity from Short Paired Reads
Author: 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; Shlyakhter, Ilya; Young, Sarah

Note: Order does not necessarily reflect citation order of authors.

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.
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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).
Published Version: doi:10.1186/gb-2009-10-10-r103
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784318/pdf/
Terms of Use: 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
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:4551386

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  • FAS Scholarly Articles [7362]
    Peer reviewed scholarly articles from the Faculty of Arts and Sciences of Harvard University
 
 

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