Rare disease and cancer analysis models for sequencing data. Scientist at PacBio. Art school survivor. Views my own. genomic.social/@csaunders
Joined July 2010
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15 Photos and videos
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!
pacb.com/wp-content/uploads/…
Final #ASHG24 poster session is starting now, come say hi if you’re interested in long read PGx, poster 7021!
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Chris Saunders retweeted
8 Nov 2024
Xiao talking now about using Paraphase and HiFi data to resolve segmental duplications genome wide
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Chris Saunders retweeted
7 Nov 2024
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.
pacb.com/press_releases/pacb…
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Chris Saunders retweeted
7 Nov 2024
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Chris Saunders retweeted
28 Oct 2024
I'm happy to announce that SVTopo, a new computational tool from PacBio (github.com/PacificBioscience…), 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
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15 Oct 2024
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/PacificBioscience…
20 Aug 2024
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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Chris Saunders retweeted
4 Oct 2024
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 biorxiv.org/content/10.1101/…
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Chris Saunders retweeted
3 Oct 2024
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!
biorxiv.org/content/10.1101/…
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Chris Saunders retweeted
26 Sep 2024
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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Chris Saunders retweeted
24 Sep 2024
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: bit.ly/3yVbFuG
#PacBio
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Chris Saunders retweeted
21 Aug 2024
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.
20 Aug 2024
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
doi.org/10.1101/2024.08.19.6…
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21 Aug 2024
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:
x.com/ctsa11/status/18259575…
20 Aug 2024
Local assembly of @PacBio HiFi for exceptionally accurate structural variant detection. Work by @ctsa11 @holtjma @nothingclever @dnb_hopkins @MikeEberle
software: github.com/PacificBioscience…
Preprint:
doi.org/10.1101/2024.08.19.6…
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20 Aug 2024
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
doi.org/10.1101/2024.08.19.6…
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20 Aug 2024
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/PacificBioscience…
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20 Aug 2024
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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