Pacific Biosciences of California Inc (PACB)

[Paulieme]

Published online 25 November 2014=== Long-read, whole-genome shotgun sequence data for five model organisms
http://www.nature.com/articles/sdata201445 -- Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing
Konstantin Berlin, Sergey Koren, Chen-Shan Chin, James Drake, Jane M Landolin, Adam M Phillippy
doi: http://dx.doi.org/10.1101/008003
Konstantin BerlinUniversity of Maryland, College Park, MD; Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteSergey KorenNational Biodefense Analysis and Countermeasures Center; Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteChen-Shan ChinPacific Biosciences Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJames DrakePacific Biosciences Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJane M LandolinPacific Biosciences Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdam M PhillippyNational Biodefense Analysis and Countermeasures Center; Find this author on Google ScholarFind this author on PubMedSearch for this author on this site
AbstractInfo/HistoryMetricsData Supplements?Preview PDF Abstract
We report reference-grade de novo assemblies of four model organisms and the human genome from single-molecule, real-time (SMRT) sequencing. Long-read SMRT sequencing is routinely used to finish microbial genomes, but the available assembly methods have not scaled well to larger genomes. Here we introduce the MinHash Alignment Process (MHAP) for efficient overlapping of noisy, long reads using probabilistic, locality-sensitive hashing. Together with Celera Assembler, MHAP was used to reconstruct the genomes of Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster, and human from high-coverage SMRT sequencing. The resulting assemblies include fully resolved chromosome arms and close persistent gaps in these important reference genomes, including heterochromatic and telomeric transition sequences. For D. melanogaster, MHAP achieved a 600-fold speedup relative to prior methods and a cloud computing cost of a few hundred dollars. These results demonstrate that single-molecule sequencing alone can produce near-complete eukaryotic genomes at modest cost.

http://biorxiv.org/content/early/2014/08/14/008003