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

Iain MacCallum, 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

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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).

Original languageEnglish
Article number103
JournalGenome biology
Volume10
Issue number10
DOIs
Publication statusPublished - 1 Oct 2009

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ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

MacCallum, I., Przybylski, D., Gnerre, S., Burton, J., Shlyakhter, I., Gnirke, A., Malek, J., McKernan, K., Ranade, S., Shea, T. P., Williams, L., Young, S., Nusbaum, C., & Jaffe, D. B. (2009). ALLPATHS 2: Small genomes assembled accurately and with high continuity from short paired reads. Genome biology, 10(10), [103]. https://doi.org/10.1186/gb-2009-10-10-r103