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

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).

DOI: 10.1186/gb-2009-10-10-r103

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@inproceedings{MacCallum2009ALLPATHS2S, title={ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads}, author={Iain MacCallum and Dariusz Przybylski and Sante Gnerre and Joshua N. Burton and Ilya Shlyakhter and Andreas Gnirke and Joel A. Malek and Kevin Mckernan and Swati S Ranade and Terrance P. Shea and Louise J S Williams and Sarah Young and Chad Nusbaum and David B. Jaffe}, booktitle={Genome Biology}, year={2009} }