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closeNewbler algorithm
Posted by lexnederbragt on 14 Dec 2011 at 12:55 GMT
Newbler, ABySS, and Soapdenovo all use kmers with a de Bruijn-graph-based mapping to form contigs
http://plosone.org/article/info:doi/10.1371/journal.pone.0028436#article1.body1.sec3.sec2.p4
Contrary to the manuscript text, Newbler does not use a de Bruijn graph approach for assembly of contigs. It instead uses Overlap Layout Consensus (OLC).
RE: Newbler algorithm
rogerab replied to lexnederbragt on 14 Dec 2011 at 17:24 GMT
I wrote this based on the article describing the Newbler algorithm, as well as others, in Nature Methods, 2009, by Paul Flicek and Ewan Birney. I have no primary knowledge of the algorithm, but what they describe does seem to make use of the Eulerian path methods that are part of the De Bruijn algorithms. And they do specifically refer to it as the first to exploit the technology, referring to the use of kmers and the de Bruijn graphing method.