Chris Saunders
@ctsa11
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Rare disease and cancer analysis models for sequencing data. Scientist at PacBio. Art school survivor. Views my own. https://t.co/5iXEF3EMSK
San Diego, CA
Joined July 2010
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
Final #ASHG24 poster session is starting now, come say hi if you’re interested in long read PGx, poster 7021!
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Xiao talking now about using Paraphase and HiFi data to resolve segmental duplications genome wide
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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
pacb.com
Priced at just $169,000 Vega is designed to make highly accurate long-read sequencing accessible to any laboratory Translations: Japanese | Chinese | Korean MENLO PARK, Calif., Nov. 06, 2024...
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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
github.com
Complex structural variant visualization for HiFi sequencing data - PacificBiosciences/SVTopo
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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
github.com
Joint structural variant and copy number variant caller for HiFi sequencing data - PacificBiosciences/sawfish
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:
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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
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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
biorxiv.org
Recent advances in genome sequencing have improved variant calling in complex regions of the human genome. However, it is difficult to quantify variant calling performance since existing standards...
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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!
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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.
Unlock the complexities of soil communities with #HiFisequencing on #Revio. Discover how to obtain high-quality MAGs with more data and lower costs than ever before. Register now: https://t.co/IA8KSVlFva
#PacBio
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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.
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
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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
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
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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.
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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
github.com
Joint structural variant and copy number variant caller for HiFi sequencing data - PacificBiosciences/sawfish
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We also demonstrate how sawfish’s quality model can be used to select for a 'sawfish HQ' call set, with an even higher proportion of concordant SVs (86%), while still retaining over 27000 pedigree-concordant SVs.
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To assess joint-calling, we examined genotype pedigree concordance across SV calls from the 2nd and 3rd generations of CEPH-1463, finding that sawfish has over 9000 more pedigree-concordant calls than other methods while retaining the highest proportion of concordant SVs:
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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:
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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
biorxiv.org
Motivation Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accuracy, long-read sequencing can substantially improve...
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