Tim Dunn

New vcfdist paper on bioRxiv! Key Takeaways: 1) Jointly evaluating small and structural variants decreases measured FN+FP by 20-50% 2) 43-92% of phasing flip "errors" are FP due to variant representations More below Code: github.com/TimD1/vcfdist Paper: biorxiv.org/content/10.110…

🚨Apparently all NIH Study Sections have been suspended indefinitely. For those who don’t know, this means there won’t be any review of grants submitted to NIH Depending on how long this goes on for, this could lead to an interruption in billions in research funding.

Finally took the time to create a BlueSky account, you can follow me @timd.one

@i000 @strnr Thank you!

@strnr Vcfdist brought much needed clarity in terms of complex variant normalization @T1MD1 very important work in clinical setting

Jointly benchmarking small and structural variant calls with vcfdist genomebiology.biomedcentral.com/articles/10.11… 🧬🖥️ github.com/TimD1/vcfdist

After nearly six months waiting for review, our extension to vcfdist was finally published in BMC Genome Biology this week! genomebiology.biomedcentral.com/articles/10.11…

@AaronPomerantz @iiSeymour @rrwick @nanopore Cool! With 2/3 errors occurring in the same "GAGCTCC" motif, it makes me wonder if there's some kind of base mod, or if the motif is just underrepresented in the training data.

A slide is worth a thousand words. At #ASMicrobe, @rrwick shared a fantastic presentation 'In Pursuit of Perfection, bacterial genome assembly from 2016 to today', including this recent Klebsiella isolate genome assembly of 99.99995% identity (Q63.0) using @nanopore data alone

Climate experts were increasingly saying that keeping heating below 1.5C is near impossible, yet it remains the global goal. So I asked hundreds of top IPCC scientists what they thought. What they said shocked even me… 🧵 1/n #ClimateCrisis

@baobaoyaobaobao @fulcrumgenomics Thanks Emily!

@T1MD1 @fulcrumgenomics CONGRATULATIONS TIM 🎉🎉🎉🎉🎉

I'm thrilled to announce that I successfully defended my PhD thesis today, "Improving select applications of long-read DNA sequencing"! After graduating, I'll be joining @fulcrumgenomics as a Senior Bioinformatics Scientist. I can't wait to see what this next chapter brings!

Excited to see a new benchmarking analysis using vcfdist!

Mandatory reading and surprising results from Michael Hall and colleagues - much better SNP/indel calling results from latest nanopore (beating illumina), and deep learning methods really doing well. Extremely thorough work biorxiv.org/content/10.110…

@viveksrm24 @fredhutch Congrats Vivek!

Very pleased to share that I’ll be joining the @fredhutch data science lab as a clinical data scientist later this month! I’m so excited for the chance to have a translational impact on biomedical discovery from bench to bedside through the development of clinical NLP products.

Finally got around to adding vcfdist into bioconda. Installation is now as easy as `conda install vcfdist`. github.com/TimD1/vcfdist

Google is donating $1M to the @rust_foundation to improve C++/Rust interoperability. This is big news!

Excited to announce that our accompanying paper on HiPhase has been published today, I'll highlight some of the additions in this thread! #PacBio #HiFi “HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing”: doi.org/10.1093/bioinf…

Comparison to prior work: lower measured FP and FN rates than vcfeval or Truvari, and similar results to Truvari refine (WFA/MAFFT). Truvari is faster and works with larger variants, but skips SNPs and the more accurate WFA/MAFFT versions don't scale to large BED regions

As noted above, joint evaluations reduce measured false negative and false positive variant calls across the board: by 28.1% for SNPs, 19.1% for INDELs, and 52.4% for SVs over 50 bases on 3 whole-genome datasets.

New vcfdist paper on bioRxiv! Key Takeaways: 1) Jointly evaluating small and structural variants decreases measured FN+FP by 20-50% 2) 43-92% of phasing flip "errors" are FP due to variant representations More below Code: github.com/TimD1/vcfdist Paper: biorxiv.org/content/10.110…