It's great being able to connect with my fellow public health bioinformaticians at the AMD Leads Meeting in Atlanta!

Working from home with a sick-kid-that-feels-fine is such an adventure. Features: fever that reduces with acetaminophen random infrequent cough lots of energy and stir craziness

I finally fleshed out one of my python scripts into a package: daisyblast Instead of pairwise blast results, this is intended to find blast hits that are shared by _n_ queries (like a daisy chain!). I can create dotplots of multiple samples

This is my first time working with NeighborNet (part of phangorn), and I think I'm going to need to do some reading so that 1) this makes sense to me, and 2) I can explain it to my collaborators

I have finally done it! I finished a rough draft for a manuscript and sent to to co-authors for editing. I may have it submitted by the end of this year!

I had an EPI contact me to see if any isolates were clustering with 2024CK-00004 and 2024CK-00250 for EPI reasons. Pathogen Detection has these two isolates in the same cluster, making this question relatively easy to answer.

I probably need some different colors, but I've made a graph detailing the number of AMR genes we've seen in organisms that we've sequenced for the last few months.

"WGS-informed prevention could hypothetically generate net savings of €1.35 million annually if transmission was stopped once a clonal isolate was detected in a second patient." I think that translates to ~1.5 million US dollars

And today's (useless) figure is that the mean depth observed in a bam file is linearly associated with the number of reads in the corresponding fastq files.

I had 18 samples (33 million+ reads) of SARS-CoV-2 amplicon-based sequencing that would not create a decent consensus fasta after aligning with `bbmap` and trimming/consensus generation with `ivar`, but would if I tweaked the pipeline a bit. /

Just finished updating my prokaryotic representative genome mash reference coinciding with refseq version 232 🧬🖥️🦠

Conda is an open-source command-line system for package and environment management. It's free, and generally does not need admin privileges. Since I helped someone install conda today, I'll share the process here. /

Awesome to see the transparent, systematic, and evidence-based approach behind the WHO Bacterial Priority Pathogens List 2024 out in the Lancet Infectious Diseases www.thelancet.com/journals/lan...

We have a new APHL fellow working with us! @robbysainsbury.bsky.social is going to do some great things!

We've successfully sequenced *6* Movbillivirus hominis (the virus that causes measles) found in local patients. The fastq and fasta files will eventually be found in BioProject PRJNA1293457. /

Currently having an intern test how normalization impacts coverage for amplicon libraries. This one is normalized to 500X coverage.

I watched this video of a concert that was part of Game Developers Conference (GDC), and the back of my mind won't stop trying to find a Public Health or Bioinformatics Conference equivalent.

It's 8+1 day, so it's a day to feature Cecret (Lake)

I finally have slurm up on both of my linux workstations! (please clap)

Today's #soundtrack is from Abzu. This #ost is both orchestral and Choral. Tracks transition from tranquil, meditative tones to swelling, dramatic climaxes #VideoGameMusic

Just finished updating my prokaryotic representative genome mash reference coinciding with refseq version 231 🧬🖥️🦠

Have I done primer design before? Yes. Have I added in probe design before? Yes. Has it been over a decade? Also, Yes. Wish me luck!

Today's #soundtrack is from Final Fantasy Crystal Chronicles. This #ost is mostly calm and whimsical instrumental pieces. #VideoGameMusic

Today's #soundtrack is from Drakengard 2. The Drakengard 2 #ost is dramatic and orchestral, which I think is great for creative or minimal-focus work. It also makes the day feel like a fantasy epic. #VideoGameMusic

I kept my name because it comes with a theme song. I wish everyone everywhere the same privilege, even if their reasons are more valid.

I love being able to video conference in for friend's thesis defenses! Congratulations Amy Sawyer! (Not on bluesky... yet)

Today's #soundtrack is from Batman: Arkham Shadow. This #ost has a full orchestra and choir for dramatic and tense pieces. #VideoGameMusic

For the first time in _forever_, I took a long trip outside of cell service and wifi range. It was an immensely refreshing experience. Also, I apologize to everyone who needed an email from me last week.

Today's #soundtrack (s) are from Age of Empires (AoE) I and II. There isn't enough music with just one of them. I's #ost blends traditional-sounding rhythms and instruments with synthesized sounds. II is more melodic and layered than I. #VideoGameMusic

Today's #soundtrack is from Octopath Traveler. This #ost consists of orchestral and folk-inspired pieces. #VideoGameMusic

I am working with an intern this summer, and I showed them how to install and use conda. I recommend using separate environments for different conda tools For example: conda create -n seqkit conda activate seqkit conda install -c bioconda seqkit (or conda create -n seqkit -c bioconda seqkit)

Documentation always takes me 10X longer than I think it should, but I finally created a wiki page with information on what tools I use and how they help me evaluate nanopore assemblies.

Today's #soundtrack is from the Final Fantasy IX. It's a lot of light instrumental pieces featuring lutes, harpsichords, woodwinds, and a lot of other string instruments.

Today's #soundtrack is from the Witcher 2. This OST is largely instrumental with mostly atmospheric, but also some intense dramatic pieces.

I would sequence them

Today's #soundtrack is from Ori and the Blind Forest. This OST is orchestral that shifts between calm, melancholic moments and intense sequences.

Today's #soundtrack is Hotline Miami. It's a bouncy electronic piece to keep me on track for the first day of a short week.

I have so many cool outbreaks that I want to put together for publication. It is so hard to find time to put together data into something shareable.

I think the _idea_ of using cockroaches to study the microbiome great. Cockroaches eat whatever and can be sterilized/germ free in ways other model organisms can't be. 🤯 #SFA2F

I helped work on this! Basically, containers (like those used by docker, podman, and singularity) provide consistent environments for bioinformatic tools so that public health bioinformaticians can do the work they need to do.

Next year #SFA2F turns 20?!?!?

Today's #soundtrack is Elden Ring, especially the violin pieces.

I thought this facility had gotten their #CRPA under control, but two new patients appear to cluster with the ones from 2022 and 2023. (Also, I work with some great epis who are on top of this in order to keep our healthcare facilities safe) 🧬🖥️🦠

One of the last sessions of #APHL2025 included a informal contest between bench microbiologists and bioinformaticians. I think they missed one key point that I'll add here (over a day late): in a zombie apocalypse, you'll want a bench scientist over a bioinformatician.

Just finished updating my mash reference for refseq 230. 🧬🖥️🦠

I didn't know dog rescues could team up with conferences, but it was pretty awesome to have some dogs attending #APHL2025

Poster is up! Rapid poster presentation done! My #APHL2025 poster is 189. Come talk to me about containers!

I didn't bring any of my versions, but we should have "Monopoly" tournament one of these evenings. #APHL2025

Let #APHL2025 begin!

Remember when you first learned about genetics at school? All those fascinating examples of human traits that are each apparently determined by just a single gene? Time to check in on some of your favourites to see how they’re doing. 🧬🧵🧪 1/n