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A common question about our metagenomics work is the extraction method. Anyone interested, we use a Qiagen TissueLyser with speed setting 21 cycles/s and we use time as the variable for assessing DNA fragment size not frequency.

Latest HiFi cell, DNA from blood of a water buffalo. Total yield 1.88M reads, 38.7 Gbase HiFi.

comparison with a protist enrichment library from cattle rumen, size selection on ELF instead of BluePippin. Total yield 1.86M reads, 35.4 Gbase HiFi

FWIW update: the exact same buffalo library with new binding loaded at same concentration but for some reason had lower polymerase speed and produced 30.4 Gb from the same number of productive ZMW (i.e. it was the conversion from P1 ZMW to HiFi read that was the difference)

A little late to the party but first HiFi cell that produced >40 Gbase Q31 from 1.87M reads 22.5Kb avg, total 42.2 Gbase. Cattle blood DNA.

As opposed to optimized for read length, this generated 29 Gbase with 28 Kbase mean HiFi read length (pig fetal bicep DNA)

Team #T2T stopped by chilly Nebraska this week looking for some more genomes to finish and found lots of volunteers 🐮 Thanks for the great workshop Tim Smith!

Thanks to my partners Brenda Murdoch and Stephanie McKay in organizing the Ruminant T2T workshop last week ! Also to support staff that made it run smoothly

Those who stayed to join the sandhill crane migration outing were rewarded with a particularly spectacular night as a pair of coyotes kept rousting the cranes into the air. I'd load video but twitter seems incapable of that today

Also thanks to the all the speakers: Adam Phillippy, Karen Miga, Rachel O'Neill, Erich Jarvis, Klaus Koepfli, Yana Safonova, Tamara Potopova, Sergey Koren, Arang Rhie, and Ben Rosen, and to all of the attendees in person (pic) or virtual !

This works better. Sandhill cranes make a weird dinosaur-like sound. Hard to see in the video how large they are but they are big birds. Thanks to Amy Sandeen for getting us the "VIP" heated bird blind and bringing us wine and beer while we waited for the cranes to come in.

In a world where you can be anything, always be a number 50!

New white paper describing the Bovine Pangenome Consortium is out ! genomebiology.biomedcentral.com/articles/10.11…

Induction into the USDA Agricultural Research Service Science Hall of Fame last March. Thanks to all my support staff over the years that led to this. Especially Bob Lee, happy retirement Bob ! Also a long list of excellent collaborators from academia, government, and industry.

Ruminant T2T project article is finally out ! nature.com/articles/s4158…

Thanks to everyone who helped with bringing this to fruition, especially Rachel for crafting the main figure

Congratulations Temitayo Olagunju ! The cattle/sheep complete Y chromosomes paper is live at Nature Comms rdcu.be/dVikS

latest pub with Beth Shapiro, the hybrid bison/cattle breed is not actually a hybrid. First experience publishing in eLife. elifesciences.org/reviewed-prepr…

I'm retiring on September 30, last day my USDA email will work is Wednesday, April 30 (two more days!)

New career starting, very excited about helping where I can !