Lee Katz

Lee Katz

@lskatz.github.io

Co host of the Micro Binfie podcast

1.6K followers319 following172 posts

Lee Katz reposted

Daniel Anderson
@danderson123.bsky.social

1/3 I'm delighted to share that Amira, a tool I worked on during my PhD, has been published in Genome Biology! 🎉 Genome assembly often struggles to reconstruct AMR markers, meaning we can miss them entirely. Amira detects them more sensitively than existing approaches.

Lee Katz reposted

Kristian G. Andersen
@kgandersen.bsky.social

This is the worst news I have heard in a very long time - what a tragic loss. @helenbranswell.bsky.social was, unquestionably, _the_ best in the field and just a wonderful person. Condolences to her family and colleagues - she'll be sorely missed. www.statnews.com/2026/10/13/h...

statnews.comHelen Branswell, whose reporting on infectious diseases and public health drew acclaim, dies at 69Helen Branswell, STAT's infectious disease reporter who earned the respect of experts and public health officials with her accessible, prescient dispatches, has died at age 69.

Lee Katz reposted

Apoorva Mandavilli
@apoorvanyt.bsky.social

I’ve been reporting on the CDC for years, and have written about many of its troubles over the past year. I was still shocked by the extent of the staff losses and political interference I found when reporting this one. www.nytimes.com/2026/09/26/h...

nytimes.com‘Zombified’ C.D.C., Hobbled by Cuts, Struggles to Fulfill Scientific Mission (Gift Article)The agency has lost its independence and nearly a third of its staff, as Health Secretary Robert F. Kennedy Jr. and associates have tightened control.
Lee Katz
@lskatz.github.io

I'm trying to crowd source notes at #ipnc2026 and so please DM me if you're at the meeting and hopefully if you can help with notes

Lee Katz
@lskatz.github.io

I'll do one more. Fasten is now just about as fast as trusted unix utilities for sorting sequences. Original vs new version of Fasten.

Lee Katz
@lskatz.github.io

Here is the original read cleaning speed vs the new read cleaning speed. As compared to seqtk, fasten now performs in the same magnitude.

Lee Katz reposted

Lee Katz
@lskatz.github.io

I wrote a post about how this all came together. About 20 iterations, switching between Claude conversational mode for structure and the GitHub agent for targeted fixes once I could see things rendering. Found that split worked surprisingly well. lskatz.github.io/personal/202...

lskatz.github.ioYearbook templateMy wife volunteers on the school yearbook committee. Her job is to solicit pictures, organize them, and help with the yearbook layout. She and the other volunteers work in a proprietary web tool. Watc...
Lee Katz@lskatz.github.io

My wife volunteers on the school yearbook committee, working in a proprietary web tool. Watching her, I got curious: what if a yearbook was just a Git repo? So I built one as a Jekyll template. lskatz.github.io/yearbook-tem...

Lee Katz reposted

Andrew Lawrence
@ndrew.bsky.social

the food safety stuff is another reminder that a large, huge, gigantic part of being a republican is going “lmao why are we spending money to prevent horrifying disasters from happening if they never happen 🤪”

Lee Katz
@lskatz.github.io

Early versions were known as the Kapsak Spectac. Congratulations team!!

Jess Chen@drjesschen.bsky.social

Hurray!! Big congrats to Arzoo and Mo from my team for developing this pipeline and getting it out there! Thanks to Justin, Peyton, @curtiskapsak.bsky.social and @lskatz.github.io their support of this work!

Lee Katz
@lskatz.github.io

🦑 Kalamari v5.9 adds new outbreak‑relevant viral genomes to the curated set. This includes topical organisms related to ongoing outbreaks: measles, hantavirus, and ebola. 🔗 github.com/lskatz/Kalam...

github.comRelease v5.9 now with ebola, hentavirus, and measles (oh my!) · lskatz/KalamariWhat's Changed Fix build-sketch CI failure due to slash in github.ref_name for PRs by @Copilot in #72 Add Bundibugyo ebolavirus reference genome to Kalamari chromosome catalog by @Copilot in #80 F...

Lee Katz reposted

Alt CDC (they/them)
@altcdc.altgov.info

💉 Did you know, if you live in or are traveling to a measles outbreak area, your baby can receive the measles vaccine as early as 6 months❓ Babies under 12 mo are at highest risk for severe disease from measles. Early vaccination provides critical protection during outbreaks.

aap.orgMeasles Prevention and Control ImplementationPlease use this page to implement practices in your office to prevent and control measles spread. You’ll find details about measles vaccination recommendations, a sample, customizable measles policy,  and tips to help implement it in your office.
Lee Katz
@lskatz.github.io

It has been many years since I created Annapotater out of the frustration that there was no simple SNP annotation tool at the time. The mainstream tool required Java and if you wanted to have a custom genome, then it was also a pain.

Lee Katz
@lskatz.github.io

I gave it a silly name because I thought it was a silly project. A cross between "annotate" and "potato" which was a sort of slang term for bad camera at the time. But I also liked the name because just like a SNP, the name can be pronounced with many different variations.

Lee Katz reposted

bigdatabiology.bsky.social
@bigdatabiology.bsky.social

How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...

biorxiv.orgThe elusive resistome: a global comparison reveals large discrepancies among detection pipelinesIdentifying antibiotic resistance genes (ARGs) from metagenomic data is critical for studying antimicrobial resistance across microbial communities and pathogens. However, there is no standardized methodology for ARG annotation. Here, we compare ten commonly used ARG detection pipelines by analysing over 270 million prokaryotic genes from the Global Microbial Gene Catalogue across 13 distinct habitats. We observed up to a 45-fold difference in the number of reported ARGs, with a mean Jaccard index of only 16% between pipelines. Pipeline selection profoundly impacted downstream biological interpretations, with drastic changes to estimates of ARG relative abundance and richness, to the characterization of pan- and core-resistomes, and to the class-level composition of the inferred resistome. ARG detection pipelines make different, defensible trade-offs, and no single approach should be treated as authoritative. Therefore, users should justify and communicate choices carefully, as our analyses show that, taken uncritically, the same data can support conflicting biological and ecological interpretations. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council of Australia (NHMRC), 2031902 Australian Research Council (ARC), FT230100724 International Development Research Centre (IDRC), 109304-001 Deutsche Forschungsgemeinschaft (DFG), FO1279/6-1 Bundesministerium für Bildung und Forschung (BMBF), F01KI1909A, 01KI2404B Swedish Research Council (VR), 2024-06123, 2019-00299, 2023-01721 Knut and Alice Wallenberg Foundation, KAW 2020.0239 Swedish Foundation for Strategic Research, FFL21-0174

Lee Katz reposted

Luis Pedro Coelho
@luispedrocoelho.bsky.social

Replying to @luispedrocoelho.bsky.social

Here is the scientific thread bsky.app/profile/did:...

bigdatabiology.bsky.social@bigdatabiology.bsky.social

How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...

biorxiv.orgThe elusive resistome: a global comparison reveals large discrepancies among detection pipelinesIdentifying antibiotic resistance genes (ARGs) from metagenomic data is critical for studying antimicrobial resistance across microbial communities and pathogens. However, there is no standardized methodology for ARG annotation. Here, we compare ten commonly used ARG detection pipelines by analysing over 270 million prokaryotic genes from the Global Microbial Gene Catalogue across 13 distinct habitats. We observed up to a 45-fold difference in the number of reported ARGs, with a mean Jaccard index of only 16% between pipelines. Pipeline selection profoundly impacted downstream biological interpretations, with drastic changes to estimates of ARG relative abundance and richness, to the characterization of pan- and core-resistomes, and to the class-level composition of the inferred resistome. ARG detection pipelines make different, defensible trade-offs, and no single approach should be treated as authoritative. Therefore, users should justify and communicate choices carefully, as our analyses show that, taken uncritically, the same data can support conflicting biological and ecological interpretations. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council of Australia (NHMRC), 2031902 Australian Research Council (ARC), FT230100724 International Development Research Centre (IDRC), 109304-001 Deutsche Forschungsgemeinschaft (DFG), FO1279/6-1 Bundesministerium für Bildung und Forschung (BMBF), F01KI1909A, 01KI2404B Swedish Research Council (VR), 2024-06123, 2019-00299, 2023-01721 Knut and Alice Wallenberg Foundation, KAW 2020.0239 Swedish Foundation for Strategic Research, FFL21-0174

Lee Katz reposted

Pathoplexus
@pathoplexus.org

1/ 🚀 Pathoplexus now supports the Andes variant of Hantavirus (ANDV). ANDV is the variant identified in the recent MV Hondius cases, & the Hantavirus variant previously identified as having occasional human-to-human transmission. pathoplexus.org/andv #hantavirus #hondius

Lee Katz reposted

Dr. Tom Frieden
@drtomfrieden.bsky.social

Hantavirus is unlikely to spiral into a pandemic. But the real story is this: WHO is on the cruise ship. It's issuing clear guidance. It's coordinating across countries. CDC has been largely silent—no guidance to doctors, no public update.

Lee Katz
@lskatz.github.io

I wrote a post about how this all came together. About 20 iterations, switching between Claude conversational mode for structure and the GitHub agent for targeted fixes once I could see things rendering. Found that split worked surprisingly well. lskatz.github.io/personal/202...

lskatz.github.ioYearbook templateMy wife volunteers on the school yearbook committee. Her job is to solicit pictures, organize them, and help with the yearbook layout. She and the other volunteers work in a proprietary web tool. Watc...
Lee Katz@lskatz.github.io

My wife volunteers on the school yearbook committee, working in a proprietary web tool. Watching her, I got curious: what if a yearbook was just a Git repo? So I built one as a Jekyll template. lskatz.github.io/yearbook-tem...

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Lee Katz
@lskatz.github.io

What's in the box: • Class / club / sports / staff pages • Auto profile pages per person • Photo galleries with people-tagging • Name search • Superlatives, year-in-review, autographs • Print-to-PDF • Auto image resize + EXIF stripping

Lee Katz
@lskatz.github.io

Caveats: this is a hobby project, not a production service. The demo uses Malcolm in the Middle characters as stand-in students. If you'd want to try it for real, the README covers privacy and hosting tradeoffs — but use at your own risk. MIT licensed: github.com/lskatz/yearb...

github.comGitHub - lskatz/yearbook-template: A template for making a yearbook through the Jekyll framework https://lskatz.github.io/yearbook-template/A template for making a yearbook through the Jekyll framework https://lskatz.github.io/yearbook-template/ - lskatz/yearbook-template
Lee Katz
@lskatz.github.io

Adding a kid is one entry in a YAML file and a photo named jane-smith.jpg. Then list jane-smith under whatever class, club, or sports team she's in. A profile page is auto-generated, listing every group she's in.

Lee Katz
@lskatz.github.io

My group is Alt CDC famous!

Alt CDC (they/them)@altcdc.altgov.info

Haemophilus influenzae type b (Hib), a vaccine preventable disease, is making a comeback. Hitting hardest among vulnerable adults facing housing instability, smoking, and substance use. 🏡 🚬 Progress isn't permanent. Let’s protect it. Keep preventable diseases-prevented. 💉 💪

cdc.govClusters of Invasive Haemophilus influenzae Type b Disease Among AdultThis report describes two clusters of invasive of Haemophilus influenzae type b among adults with special risk factors in Alaska, Oregon, and Washington.