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Back from SFAF, and Eager for More Finished Genomes

Tuesday, June 18, 2013

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 unexpected differences that are not
included in a reference genome. This idea is especially compelling in the
microbial world, where pan-genomes and horizontal gene transfer have turned the
whole idea of a single reference genome on its head.
Finishing genomes — how to generate them and how much
they cost — was another common thread. It was impressive to see how many
conference attendees were using the HGAP/Quiver method to finish all sorts of
microbial genomes. Ken Dewar from McGill University gave a presentation based
on a simple question: Can we sequence one full bacterium in one day for less
than $1,000? We were thrilled to see that PacBio’s technology is meeting his
goal. In another talk, Adam Phillippy from the National
Biodefense Analysis and Countermeasures Center said that with PacBio® technology, it’s
now cheaper to finish a microbial genome than it is to publish one.  Phillippy noted that once reads exceed 7 kb
for microbial genomes, assembly complexity is drastically reduced; using the XL
chemistry, 40 percent of their PacBio reads have been at least that long. He
and other speakers noted that they have been getting Q60 scores from their
PacBio data with the latest hardware and software upgrades.
Most of all, we were inspired by so much compelling
science and the community’s renewed commitment to finished genomes. Many
attendees talked about their motivation to go back to their labs and try out
these new methods for finishing microbial genomes, especially since the whole
process can now be automated.

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