At SFAF 2014, Great Science and High-Quality Genomes
Friday, June 27, 2014
It’s been a busy start to the summer, but we’re still basking in the top-notch presentations and posters from the Sequencing, Finishing, and Analysis in the Future meeting last month. Hosted by Los Alamos National Laboratory in Santa Fe, this has become a premier event for scientists working on sequencing protocols, analysis, and assembly methods.
Many speakers presented data including reads from Single Molecule, Real-Time (SMRT®) Sequencing. Jeff Rogers from Baylor College of Medicine used long PacBio® reads with the PBJelly algorithm to fill gaps in many mammalian genomes, including sheep, rat, baboon, sooty mangabey, and mouse lemur. Tina Graves-Lindsay from Washington University reported work on improving the reference human genome through BAC sequencing and the use of a haploid human data set, which included PacBio’s CHM1TERT data release. James Gurtowski from Cold Spring Harbor Labs detailed improvements to genome assemblies of yeast, Arabidopsis, and various rice strains using his new algorithms, ECTools.
From our own team, Steve Turner used several data sets we’ve released publicly in the last nine months — including Arabidopsis, Drosophila, spinach, and human — as a way to demonstrate continued improvements in the PacBio chemistries. In another talk, Jason Chin, our informatics guru, spoke about the new diploid assembler called FALCON.
Other exciting talks included Rick Wilson’s keynote topic, “Recent Advances in Cancer Genomics,” where he discussed a case study on combining whole genome, exome, and RNA sequencing. The research helped guide development of a successful targeted treatment approach. Deanna Church from Personalis presented on clinical exome sequencing and the idea of diagnostic yield. This was a fascinating summary on the challenges of interpreting clinical sequencing and the need for continued improvements in the current human genome build. Finally, we really enjoyed Stephan Schuster’s talk on the fly biome. He and his colleagues have done a staggering amount of work characterizing the microbiomes present on the blow fly and their importance as a mechanical vector in the movement of bacteria.
If you couldn’t attend the meeting, we captured some of the excitement in this Storify of the two hashtags used for the conference (#SFAF14 and #SFAF2014). Enjoy!