We were thrilled to see that PacBio’s technology is meeting his goal!!!
Tuesday, June 18, 2013; Back from SFAF, and Eager for More Finished Genomes
Last month’s Sequencing, Finishing, Analysis in the Future (SFAF) meeting in Santa Fe, New Mexico, hosted by Los Alamos National Laboratory, attracted terrific scientists and we really enjoyed hearing about their work as well as sharing our own technology advances. It was great to be at a meeting where genome finishing and analysis were key themes; it was an environment where our customers’ experience with HGAP and Quiver resonated, particularly around the automated finishing of microbial genomes.
SFAF had a number of keynote speakers, including Mark Adams from the J. Craig Venter Institute, who spoke about antibiotic resistance in microbes. He noted that lateral transfer of multidrug resistance genes is creating new drug-resistant pathogens in our hospitals. A key theme in his talk was the need for comprehensive information about the genomes of these drug-resistant microbes, including the difficult-to-assemble regions such as duplications, repetitive sequence, plasmids, and so on. He said that standard strain typing does not provide enough information to distinguish the particular form of resistance between bugs. For example, plasmids and phages play a critical role in horizontal gene transfer of drug resistance genes, yet these elements are notoriously difficult to assemble with short-read NGS methods. Adams commented that PacBio’s HGAP assemblies provide both finished genomes and plasmids, which offer important clues about drug resistance mechanisms and microbial adaptation.
Throughout the conference, many speakers mentioned the challenge of reference-based sequencing when there are errors in the reference, or when the reference is not a good enough representation of the genome being sequenced and compared to it. It was apparent that the trend is shifting back to de novo sequencing, which provides more information about the organism under investigation and is more likely to pick up une