Peter Fields

What do you think about our new preprint? 🥳🥳🥳Please let us know! It’s about how geography, mode of transmission, and long-term host–parasite coevolution is shaping genomic variation in a microsporidium. @peterdfields biorxiv.org/content/10.110…

Great conference during the last two days: In person and with free coffee. I got to present a poster about my PhD project. Check it out online: doi.org/10.6084/m9.fig… Work with @peterdfields and Dieter Ebert (in prep.) #biology22basel @Biology22Basel (1/3)

@ScottTKelley BlobToolkit? blobtoolkit.genomehubs.org/blobtools2/

Bioinfo Q: Any suggestions on best alignment based methods to taxonomically classify large contigs assembled from a metagenome? Note: many of the reads are NOT highly similar to know organisms (80% tops)

@kdc509 Also see: github.com/wurmlab/flo#:~….

@kdc509 A tool I've used recently is liftoff: github.com/agshumate/Lift… so assuming minimap2 works pretty well aligning your two assemblies I'd bet it works pretty well getting the annotations over

@pastramimachine ®

@pastramimachine betterhelp for scientists?

Evolutionary Biology Field Course, Guarda, Switzerland, summer 2022. Dieter Ebert is reviving this after a 2 y hiatus. John Krebs and @hopihoekstra on the faculty! Details: evolution.unibas.ch/teaching/guard…

Cool paper on Cladoceran macroevolution from van Damme, et al. Multiple origins of predation! Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution academic.oup.com/sysbio/advance…

@mbeisen Bioconda is also used to install R packages.

A postdoc in my lab is analyzing published R repos, and, since we're mostly a Python shop, don't know what package managers people use besides renv, packrat, and R studio. Any other ones they should be looking at?

There is now enough genomic data from the US and Germany to repeat this approach to estimating Omicron-specific rate of epidemic spread. Here, we observe similar initial rapid spread in the US and Germany. 1/10 twitter.com/trvrb/status/1…

No support for a meiosis suppressor in Daphnia pulex: Comparison of linkage maps reveals normal recombination in males of obligate parthenogenetic lineages. biorxiv.org/cgi/content/sh… #bioRxiv

We've seen exceptionally rapid spread of Omicron in South Africa. Although we should expect this rapid spread to follow in other geographies, we've mostly lacked data to confirm this until recently. 1/21 twitter.com/trvrb/status/1…

@the_real_KVD wo cao!

@joelmcglothlin @BiologyCarly @jbakcoleman But is the sky blue? wnycstudios.org/podcasts/radio…

@BiologyCarly @jbakcoleman The sky is blue though and that goes with everything

Does anyone else think it’s weird that we all just walk around wearing blue pants like they aren’t BLUE PANTS

@pastramimachine Bummer. Did you get mean read lengths in the 15-20kbp range? Any ploidy uncertainty?

@pastramimachine when you say messy, do you mean more fragmented than you expected? shorter?

@pastramimachine Does an expected genome size of 2Gbp in the range you expected?

@pastramimachine I see. Doesn't look a heterozygosity issue. HiFi?