Using rustybam on PAFs for SafFire
rb trim-paf .test/asm_small.paf `#trims back alignments that align the same query sequence more than once` \ | rb break-paf --max-size 100 `#breaks the a...
My history
In 2015 I graduated from Princeton with B.S.E. in computer science and a minor in quantitative and computational biology. During my time at Princeton, I worked in the lab of Alison Gammie improving the reference genome for the yeast strain W303. In 2016 I joined the Department of Genome Sciences at the University of Washington in pursuit of a PhD, ultimately joining the lab of Evan E. Eichler to study the sequence and assembly of segmental duplications in humans and nonhuman primates. I am continued my work in the Eichler lab as a postdoctoral fellow while making contributions to the T2T and HPRC. Currently, I am in Andrew Stergachis’ lab at the University of Washington. To learn about my dog classification system see here (credit Michelle Noyes).
Recent Posts
StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps
StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps https://t.co/4BAUkqegGK #bioRxiv— bioRxiv (@biorxivp...
Segmental duplications in a complete human genome
Excited to finally share: Segmental duplications and their variation in a complete human genome! This is a product of an awesome collaboration in the T2T con...
Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads
The Eichler lab at @uwgenome has compared high-fidelity (#HiFi) and continuous long-read (#CLR) datasets, and concluded that HiFi may be the most effective s...
Long-read sequence and assembly of segmental duplications
It's out! Check out my first first author paper "Long-read sequence and assembly of segmental duplications" out today at @naturemethods (https:...