If you missed this poster session at #ASHG24, you can now view the poster online! Happy to have a chat if you're interested in long-read PGx with #PacBio!
https://t.co/0rAR1OcChc
It's official, @PacBio has launched a new benchtop sequencer!
Quick summary of the new Vega system:
- instrument = $169k
- consumables = $1100 per run
- output = 60 Gbp, 24 hr run time
This is the #HiFi sequencer #microbiology labs have been asking for.
https://t.co/RYJdUCq8SA
Today, we announced the first #PacBio benchtop long-read sequencing system, Vega. #Vega delivers all the functionality of #Revio into a compact, lower- throughput benchtop platform. https://t.co/t5fG6JVqQR
#ASHG24#ASHG2024
I'm happy to announce that SVTopo, a new computational tool from PacBio (https://t.co/W6sHuB0Ps9), is ready for you to try. SVTopo creates simple images so you can rapidly understand complex changes in genome structure. See me and learn more at ASHG 2024 in Denver, poster 1180W
We've been making steady usability updates to the sawfish SV caller thanks to user feedback, including a new feature to output all supporting reads for each SV. The latest binary, user guide, and (new) source code release are available on github here:
https://t.co/Sm80gED6HF
We assessed our new method on the recent draft GIAB SV benchmark from the T2T-HG002-Q100 assembly, finding sawfish has the highest F1-score among evaluated callers on every tested SV size range and depth level. Other callers required at least 30x depth to reach sawfish at 15x:
Whoa! “As an example of the value of this improved benchmark, we retrained DeepVariant using this data to reduce genotyping errors by ~34%.”
The Platinum Pedigree: A long-read benchmark for genetic variants | bioRxiv https://t.co/NGTc7l0dn3
Very excited to share our work on building a benchmark of all classes of variation based on the large CEPH-1463 pedigree sequenced with all the technologies. A large team effort!
https://t.co/QW9hlpXxwr
Don't miss out on this #metagenomics webinar next week!
@PacBio HiFi sequencing on Revio can be used to generate single-contig, complete MAGs from the most difficult sample type to assemble - soil.
Results for wetland and grassland soil shown here, from my talk at LAMG.
I'm happy to see sawfish now available for the community to use. Sawfish is another step towards high accuracy and consistent SV genotyping. Great work by Chris Saunders and many others.
Great sawfish clip and thanks for all your help too @zevkronenberg! ...also thanks to additional coauthors @jon_belyeu & @juniper_a_lake
Sawfish summary thread here for a quick results summary:
https://t.co/BpHbqozDkG
Finally, thanks to our early users for their helpful feedback, and to the GIAB/T2T community for ongoing development of new SV benchmarks and assessment methods, which will continue to be crucial to further improvement efforts.
Happy to introduce sawfish, a new HiFi structural variant caller emphasizing local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis contexts: 1/n
https://t.co/P3kp1QUd45
Sawfish and usage documentation is available to download from github at the following site. We have several ongoing directions to further develop the method, so all feedback is greatly appreciated and can be incorporated into future feature planning.
https://t.co/Sm80gEDExd