Method
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
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* Corresponding author: David B Jaffe jaffe@broadinstitute.org
1 Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
2 Life Technologies, Cummings Center, Beverly, MA 01915, USA
3 Current address: Department of Medical Genetics, Weill Cornell Medical College in Qatar, 24144 Al-Rayaan St., Doha, Qatar
4 Current address: Pacific Biosciences, Adams Drive, Menlo Park, CA 94025, USA
Genome Biology 2009, 10:R103 doi:10.1186/gb-2009-10-10-r103
Published: 1 October 2009Abstract
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).