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

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

Publication TypeJournal Article
Year of Publication2009
AuthorsMacCallum, I, Przybylski, D, Gnerre, S, Burton, J, Shlyakhter, I, Gnirke, A, Malek, J, McKernan, K, Ranade, S, Shea, TP, Williams, L, Young, S, Nusbaum, C, Jaffe, DB
JournalGenome Biol
Volume10
Issue10
PagesR103
Date Published2009
ISSN1474-760X
KeywordsBacteria, Base Pairing, Fungi, Genome, Genomics, Reproducibility of Results, Software
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).

URLhttp://genomebiology.com/content/10/10/R103
DOI10.1186/gb-2009-10-10-r103
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/19796385?dopt=Abstract

Alternate JournalGenome Biol.
PubMed ID19796385
PubMed Central IDPMC2784318