By Julia Karow A little less than a year after the full commercial launch of Pacific Biosciences' PacBio RS sequencer, customers and collaborators are using the system for a variety of applications, including de novo assembly of genomes and transcriptomes in combination with other types of sequencing data, variant validation, analyses of trinucleotide repeat sequences, genome methylation analysis, and targeted cancer gene resequencing. At the Advances in Genome Biology and Technology meeting in Marco Island, Fla., last month, researchers discussed their use of the platform in conference talks, poster presentations, and during a company-organized workshop. One popular application of PacBio's long single-molecule reads appears to be the de novo assembly of genomes and transcriptomes, usually in combination with other types of sequencing data. Adam Phillippy's group at the National Biodefense Analysis and Countermeasures Center in Frederick, Md., for example, has developed a hybrid error-correction and de novo assembly method that maps short reads from 454, Illumina, or Ion Torrent to the error-prone PacBio reads, improving their accuracy from about 85 percent to up to 99.9 percent. The team then assembles the corrected PacBio reads using a new version of the Celera assembler (IS 1/24/2012). Phillippy and his colleagues have applied … Continue reading
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