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
RT @MikeEberle: Xiao talking now about using Paraphase and HiFi data to resolve segmental duplications genome wide
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RT @DPortik: It's official, @PacBio has launched a new benchtop sequencer!. Quick summary of the new Vega system:.- instrument = $169k.- co….
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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RT @MorghanLucas: @PacBio introducing their new benchtop sequencer, Vega, at the #ASHG24 PacBio party 🧬👾
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RT @jon_belyeu: I'm happy to announce that SVTopo, a new computational tool from PacBio (, is ready for you to try….
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:.
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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RT @OmicsOmicsBlog: Whoa! “As an example of the value of this improved benchmark, we retrained DeepVariant using this data to reduce genoty….
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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RT @zevkronenberg: Very excited to share our work on building a benchmark of all classes of variation based on the large CEPH-1463 pedigree….
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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RT @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.….
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RT @DPortik: Don't miss out on this #metagenomics webinar next week! . @PacBio HiFi sequencing on Revio can be used to generate single-cont….
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RT @MikeEberle: I'm happy to see sawfish now available for the community to use. Sawfish is another step towards high accuracy and consiste….
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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:.
Local assembly of @PacBio HiFi for exceptionally accurate structural variant detection. Work by @ctsa11 @holtjma @nothingclever @dnb_hopkins @MikeEberle . software: Preprint:.
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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.
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.
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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