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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-10

AUTHORS

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

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). More... »

PAGES

r103

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/gb-2009-10-10-r103

DOI

http://dx.doi.org/10.1186/gb-2009-10-10-r103

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1012804464

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19796385


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