For anyone doing ONT Microbial Genomics, please take 1 minute (less?) to tell us which assembly metrics you care most about when evaluating whether an assembly is "good". We are doing a benchmark of different QC tools (barcode/adapter trimming and QC filtering). microbial-qc-survey.streamlit.app

Microbial QC Survey

A standalone Streamlit app that collects community priority weights over fourassembly-QC metrics ...

microbial-qc-survey.streamlit.app

Cool to see GigaScience Press (AKA @gigabytejournal.bsky.social) is still the GOAT in metadata quality. #1 ranking out of 28,379 publishers in this Nexus Score ranking nexus-score.vercel.app/member/23445

Our paper on efficient capped-depth downsampling is out in GigaByte! 🚀 We added a new "sweep-line" algorithm to rasusa (v3.0.0) that enforces a strict depth cap at every position, while keeping the random selection rasusa is known for. 🧵 1/4 📚 doi.org/10.46471/gig... 💻 github.com/mbhall88/ras...

Efficient downsampling of genome alignments with Rasusa

Efficient downsampling of genome alignments with Rasusa

doi.org

I took a look at how the new(ish) lr:hq preset in minimap2 impacts variant calling—i.e., if I should move to using it instead of the default map-ont for recent ONT data. mbhall88.github.io/post/minimap...

v4.0.0 of rasusa is out now in all major retailers 🛍️ github.com/mbhall88/ras... Big new feature is support for unaligned SAM/BAM/CRAM as input (and output) to the reads subcommand. You can even pass in BAM and ask for FASTQ out the other side if you're into that kind of thing.

Release v4.0.0 · mbhall88/rasusa

4.0.0 (2026-04-01) ⚠ BREAKING CHANGES reads: --output-type has been renamed to --compress-type (-Z) for the reads subcommand. The -O short flag is now used for --output-format. Features reads: s...

github.com

🐍 For all ye #snakemake users out there who want consistent, opinionated formatting of their workflows: we have just released v1.0.0 of snakefmt 🥳 The major update is that it now sorts rule directives (e.g., input, output, resources, params, shell etc.). See github.com/snakemake/sn... for more

GitHub - snakemake/snakefmt: The uncompromising Snakemake code formatter

The uncompromising Snakemake code formatter. Contribute to snakemake/snakefmt development by creating an account on GitHub.

github.com

Until joining @loolibear.bsky.social's lab in July, I embarrassingly hadn't had much experience with plasmids. So when I started, Leah said "here you go, have a look at this dataset". What a fun ride this has been. Preprint out today and thread below www.medrxiv.org/content/10.6...

Novel transposon Tn8026 acts as a global driver of transmissible linezolid resistance in Enterococcus via a linear plasmid

Linezolid is a critical last-resort antimicrobial for multidrug-resistant Enterococcus faecium , particularly against vancomycin-resistant lineages where therapeutic options are severely limited. Whil...

medrxiv.org

Does anyone else think they are seeing post-acceptance editorial changes at proof stage which are error-prone and probably due to adoption of AI?

🚨 Update to nohuman 🚨 While testing against the standard Kraken DB, I noticed Kraken was detecting far more human reads than nohuman. I realised Kraken masks low-complexity regions by default during DB construction and that setting had been left on in nohuman, leading to missing human reads.

Our method for genome size estimation from long-read overlaps is now published 🥳 academic.oup.com/bioinformati...

Genome size estimation from long read overlaps

AbstractMotivation. Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existin

academic.oup.com

New from @dgpratas.bsky.social et al. for analyzing multiple sequences in multi-FASTA format using alignment-free methodologies. Scalable to millions of sequences for pandemic research and more AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data doi.org/10.1093/giga...

AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data

AbstractBackground. Most viral genome sequences generated during the latest pandemic have presented new challenges for computational analysis. Analyzing mi

doi.org

“Clarivate’s decision rewards journals for continuing the unhelpful practice of keeping peer review information hidden and unintentionally presenting incomplete and inadequate studies as sound science and punishes those journals that are more transparent.” 👏🙌 www.coalition-s.org/blog/how-the...

How the Web of Science takes a step back

<p>The Web of Science, a major commercial indexing service of scientific journals operated by Clarivate, recently decided to remove eLife from its Science Citation Index Expanded (SCIE). eLife will on...

coalition-s.org

🌟 Excited to share my latest preprint with @lachlanjmc.bsky.social on @biorxivpreprint.bsky.social: "Genome size estimation from long read overlaps”! 🚀 Check it out here: doi.org/10.1101/2024... And find the code here: github.com/mbhall88/lrge 🧵👇

Props to eLife for sticking to their guns and essentially telling Clarivate "stuff your Journal Impact Factor, we don't want/need it and neither should anyone else". Having recently published in eLife, I can attest to the fact that their review process is smooth and high quality.

eLife@elife.bsky.social · 2y ago

As a long-term signatory of the Declaration on Research Assessment, we thank DORA for this supportive message. There has been an ongoing move away from journal-level metrics; we hope this will only accelerate now.

Join the Interdisciplinary Postdoc Fellowship Program at the European Molecular Biology Laboratory (EMBL), one of the best places to do research in modern biology and develop your career. Great opportunities for statisticians, comp. biologists, AI experts, mathem. modelers! www.embl.org/eipod-linc

Handy tip of the day: Settings->Moderation->Muted words & tags->[enter last name of buffoon who is going to be president of USA] 🧘‍♂️

For all you Pythonistas out there, if you haven't tried `uv` yet, give it a go. It will blow you mind 🤯 it is essentially `cargo` (from the Rust world) for Python! Amazing it took so long for the ecosystem to get here, but we did. Astral.sh are doing some incredible things, with incredible devs

Astral: Next-gen Python tooling

Astral builds high-performance developer tools for the Python ecosystem, starting with Ruff, an extremely fast Python linter, written in Rust.

astral.sh

Charlie Marsh@crmarsh.com · 2y ago

Looks like uv is the #1 trending Rust repo over the last month 🚀🚀🚀

Microbial Genomics journal is looking for editors at senior level (functional genomics and microbe-host interactions) and handling editors (mainly eukaryotic microbial genomics but any within journal remit welcome). If you want to know more, let me know! microbiologysociety.org/who-we-are/j....

Jobs

View the current job vacancies at the Microbiology Society.

microbiologysociety.org