Chris Saunders

Rare disease and cancer analysis models for sequencing data. Scientist at PacBio. Art school survivor. Views my own.

[Matt Holt @holtjma]

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

[Mike Eberle @MikeEberle]

Xiao talking now about using Paraphase and HiFi data to resolve segmental duplications genome wide

[Daniel Portik @DPortik]

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

[PacBio @PacBio]

Lights Camera 📷 Vega ✨! So excited to finally reveal this small but mighty sequencer. Isn’t she cute? 💖

#PacBio #ASHG24 #ASHG2024

[Morghan Lucas @MorghanLucas]

@PacBio introducing their new benchtop sequencer, Vega, at the #ASHG24 PacBio party 🧬👾

[PacBio @PacBio]

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

[Jon Belyeu @jon_belyeu]

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

[Chris Saunders @ctsa11]

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

[Chris Saunders @ctsa11]

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:

[Keith Robison @OmicsOmicsBlog]

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

[Zev Kronenberg @zevkronenberg]

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

[Mitchell R. Vollger @mrvollger]

I am going on the faculty job market this year, so if your home department is starting a search, I'd love to hear about it. Thanks!

[Daniel Portik @DPortik]

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.

[Mike Eberle @MikeEberle]

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.

[Chris Saunders @ctsa11]

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

[Zev Kronenberg @zevkronenberg]

Local assembly of @PacBio HiFi for exceptionally accurate structural variant detection. Work by @ctsa11 @holtjma @nothingclever @dnb_hopkins @MikeEberle

software: https://t.co/vtahmOqCbb
Preprint:
https://t.co/AnVyvypu1c

[Chris Saunders @ctsa11]

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.

[Chris Saunders @ctsa11]

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

[Chris Saunders @ctsa11]

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