I didn’t know until now, but I was born to decline faculty meeting calendar invites.

#FirstSabbatical

For those of you doing TRIS calibration for #CarbonateChemistry, what temperature probe do you use? We've been using this: https://fishersci.com/shop/products/traceable-platinum-ultra-accurate-digital-thermometer/15081102 but it breaks yearly.

The
@MarineEvoEcoLab
just rocked it last semester. I'm so proud.

https://www.marineevoeco.com/post/2024-06-01-what-a-semester/

@ELSimms I agree. The exchange just immediately made me think of that Far Side comic. Also why I was being cheeky saying that it could be a good sign!

WARNING: if you’re using a colored and shadowed font and a 4:3 format in PowerPoint, I’m immediately questioning how many decades old the presentation is.

Out now! A dynamic web resource for robust and #reproducible #genomics in nonmodel species
https://marineomics.github.io/

This paper in @MethodsEcolEvol describes our web resource for genomics pipelines. Examples include functional genomics, population genomics #PopGen, and genome-phenome. More pages are coming soon.
Many examples use #rstats and datasets for marine organisms. Consider contributing to the site! It's a great way to achieve broader impacts for your work.

JUST PUBLISHED: "A second unveiling: Haplotig masking of the eastern oyster genome improves population-level inference" #Evolution #Genomics #PopGen #oyster https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13801

A haplotig in an assembly occurs when a single region is split into two places in the reference. We had them everywhere in our first eastern oyster assembly! This causes a bimodal distribution of coverage. This study shows how haplotigs affect pop gen inference and how to improve the reference by masking haplotigs.

I also made an Open Science Framework repository which contains data and an open and reproducible analyses, including the patching the figures together. The OSF site is
https://osf.io/9sm76/.
The masked assembly is @ https://doi.org/10.5281/zenodo.7799622
Please reach out with any questions!

We had a lot of SNPs and used strict filtering, and I suspect these effects are more pronounced with higher tolerances for missing data.

The paper itself is paywalled (but see free link above), but the nearly identical preprint is @ https://doi.org/10.1101/2022.08.29.505626

For those of you in #conservation #genomics, we show that haplotigs reduce SNP discovery and estimates of nucleotide diversity. Haplotigs also affect estimates of population structure and outlier detection, but the impacts are more nuanced.

#Haplotigs inflate assembled #genome size and they lower coverage because each haplotig gets a portion of the true genome coverage. This give a bimodal pattern on coverage across the genome. See this publication https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2485-7

See gif: https://twitter.com/jonpuritz/status/1651218353615241221?s=46

Happy to share a new publication from the @MarineEvoEcoLab describing the eastern #oyster🦪 #genome assembly.

We also describe a methodology for detecting and masking haplotigs in existing genome assemblies.

https://onlinelibrary.wiley.com/share/author/EPYJHU9F8RJ4GV6QFY4B?target=10.1111/1755-0998.13801

So what are #haplotigs? Most #genome assemblies are haploid, meaning that there is one copy of sequence for each location in the genome. Haplotigs are when allelic sequence (sequence per genome copy) are incorporated by mistake into an assembly.

The Covid rebound right on my day 10 test (negative test day 6 and day 8). A cruel trick on par with Groundhog Day. 10 more days of the guest bed…

Any ERC-funded folks out there interested in collaborating?

https://www.nsf.gov/pubs/2023/nsf23085/nsf23085.jsp?WT.mc_ev=click&WT.mc_id=&utm_medium=email&utm_source=govdelivery

@gringene exactly. First symptoms were about 16 hours after the train ride. Possible but unlikely I caught it on the train.

@eljefedsecurit bivalent booster in Sep 2022

@kentindell @rpavlik @revk here’s my CO2 monitor for the conference. I didn’t have it at the poster session which was likely as high as the peak.

@gringene Amtrak, six hour ride on NE corridor. I don’t think exposure happened there because of symptom timing.

@CStamp alt text added thanks.

I got this Amazin' #Mets special-edition Queens Public Library card!
#lgm #libraries