iiinova — where your digital self keeps evolving

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sylvain Brisse @sylvainbrisse.bsky.social · 30/11/2025

Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

doi.org

Life Identification Numbers: A bacterial strain nomenclature approach

Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

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Torsten Seemann @torstenseemann.bsky.social · 13/12/2025

💾 Shovill 1.4.1 has been released! The best way to de novo assemble microbial genomes from Illumina FASTQ. Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking. #bioinformatiocs #genomics #microbiology github.com/tseemann/sho...

github.com

Releases · tseemann/shovill

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads - tseemann/shovill

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ace-gtdb.bsky.social @ace-gtdb.bsky.social · 11/12/2025

The GTDB website now has an ANI calculator based on skani that supports uploading of user genomes. Try it at gtdb.ecogenomic.org/tools/skani. Find more information about @jimshaw.bsky.social fantastic tool at www.nature.com/articles/s41....

gtdb.ecogenomic.org

GTDB - skani calculator

An interface to compute pairwise ANI of NCBI genomes using the GTDB taxonomy.

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Ben Langmead @benlangmead.bsky.social · 03/12/2025

Kraken 2 (K2) community: we are giving more attention to our new `k2` wrapper, and a NEW functionality since 2.17.0 is: you can build several component K2 indexes, e.g. each covering a different Refseq database, and then query them all at once... github.com/DerrickWood/... 1/6

github.com

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Javier Santoyo @jsantoyo.bsky.social · 02/12/2025

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes. #ProkaryoticGenomes #AnnotatedGenomes #Bioinformatics #Genomics #NAR @narjournal.bsky.social 🧪🧬 🖥️ academic.oup.com/nar/advance-...

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Waggoner Lab @labwaggoner.bsky.social · 14/11/2025

A gene-editing approach enables modification of bacteria within the mouse gut @science.org @harriswang.bsky.social @columbiauniversity.bsky.social @shsternberg.bsky.social www.science.org/doi/10.1126/... www.science.org/doi/10.1126/...

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Ben Langmead @benlangmead.bsky.social · 30/10/2025

October 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2 Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.

benlangmead.github.io

Index zone by BenLangmead

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FEMS @femsmicro.org · 22/10/2025

Help shape the future of microbiology in Europe. FEMS is conducting a survey to better understand the needs of microbiologists. Your input will help identify key challenges & ensure the community’s voice is heard across Europe. Complete it today and share with your network: 🔗 buff.ly/5eCowPX

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Christian Kost @kostchristian.bsky.social · 15/10/2025

#microsky #mevosky @spp2389.bsky.social A PhD position is available in my lab to work on: Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria. Please RT Deadline: 12.11.25 More infos 👇 shorturl.at/rAKAT

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Zarja Muršič @zarja.bsky.social · 24/09/2025

Že tri leta se je tole pripravljalo v moji glavi Jutri izide prva epizoda okoljskega podkasta Na tankem ledu. Potem sem zavlačevala, kolikor sem lahko in si še za danes pustila zadnje ure montaže. Seveda ni popoln, ampak nekje moramo začet. metinalista.si/na-tankem-le...

metinalista.si

Na tankem ledu - Metina lista

Na Metino listo prihaja nov okoljski podkast Na tankem ledu. V njem znanstvena komunikatorka Zarja Muršič in novinarka Katarina Oblak preverjata, kako naša družba lovi ravnotežje na planetu, ki smo ga...

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FEMS @femsmicro.org · 17/07/2025

Thank you for being part of day three at FEMS MICRO Milan. That wraps up another inspiring day of learning and connection! Catch the highlights video and get ready for more exciting sessions tomorrow. #FEMSMICRO #FEMS2025

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FEMS @femsmicro.org · 15/07/2025

That wraps up day two at FEMS MICRO Milan. #MagnifyingMicrobialImpact Watch today’s highlights video and catch up on key moments. See you tomorrow for more microbiology insights and connections. #FEMS2025 #FEMSMICRO #FEMSMICRO2025

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FEMS @femsmicro.org · 14/07/2025

What an inspiring first day at FEMS MICRO Milan! We heard from FEMS Pres. Antonio Ventosa at the Opening while former Pres. Hilary Lappin-Scott helped connect new attendees. Thanks to keynotes Profs. Carmen Buchrieser and Gian Rossolini for sharing their expertise. #FEMS2025

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