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. 2009;10(10):R103.
doi: 10.1186/gb-2009-10-10-r103. Epub 2009 Oct 1.

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

Iain Maccallum  1 , Dariusz Przybylski, Sante Gnerre, Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, Kevin McKernan, Swati Ranade, Terrance P Shea, Louise Williams, Sarah Young, Chad Nusbaum, David B Jaffe
Affiliations

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

Iain Maccallum et al. Genome Biol. 2009.

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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Figures

Figure 1
Figure 1
The ALLPATHS assembly of S. aureus. Each edge represents a contiguous and unambiguous sequence of bases and, for this assembly, each component is its own scaffold. Longer edges are in red, short edges in gray. The sizes of the gray edges and regions are in bases. Several key features are called out in blue boxes. Five short sequences totaling 9 kb are not shown. Images of the graphs for all five ALLPATHS assemblies of this paper are available at [16].
See this image and copyright information in PMC

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