Jacques Dainat's Avatar

Jacques Dainat

@jacquesdainat

PhD Bioinformatics, Bioinformatician at @IRD_fr previously @Alcediag_Alcen and @NBISwe @scilifelab @uppsalauni, Annotation Assembly Epigenetic Pipeline Software Reproducibility https://github.com/Juke34

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11.11.2024
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Latest posts by Jacques Dainat @jacquesdainat

Pick a License, Not Any License Article de Paired Ends (Stephen Turner's blog)

📝 Pick a License, Not Any License
✍️ Paired Ends (Stephen Turner's blog)

16.02.2026 04:11 👍 0 🔁 1 💬 0 📌 0
GitHub - Juke34/AliNe: Nextflow Alignment Pipeline - from fastq.gz to sorted bam/cram with ease Nextflow Alignment Pipeline - from fastq.gz to sorted bam/cram with ease - Juke34/AliNe

🚀 AliNe v1.6.0 is out!

✨ Now featuring:
• Up to 20 alignment algorithms
• CRAM output support
• New parameter to filter unmapped reads
• Automatic TSV comparison table generated when statistics are enabled

github.com/Juke34/AliNe

05.02.2026 16:57 👍 2 🔁 0 💬 0 📌 0
Scientific production in the era of large language models Article de Paired Ends (Stephen Turner's blog)

📝 Scientific production in the era of large language models
✍️ Paired Ends (Stephen Turner's blog)

27.01.2026 09:36 👍 0 🔁 1 💬 0 📌 0
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nf-core/proteinfamilies: A scalable pipeline for the generation of protein families academic.oup.com/gigascience/... 🧬💻🧪

27.01.2026 15:01 👍 3 🔁 1 💬 0 📌 0
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BIOCONDA ... 😈😅

22.01.2026 15:40 👍 0 🔁 0 💬 0 📌 0
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GitHub - amrei-bp/readme_playground: ✍ A collection of options to spice up your README's. ✍ A collection of options to spice up your README's. - amrei-bp/readme_playground

Want to customize your GitHub README/profile page? 🙂
This README playground by @amrei-bp is a great resource to experiment.
github.com/amrei-bp/rea...

14.01.2026 09:40 👍 0 🔁 0 💬 0 📌 0
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Really liking the idea and output of GAQETv2 - such a cool tool for structural genome annotation QC!!
www.protocols.io/view/structu...

26.11.2025 10:42 👍 2 🔁 1 💬 0 📌 0
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Characterization and comparative genome analysis of a new Tequintavirus isolated on Salmonella enterica serotype Tennessee - BMC Research Notes Objective The rise in multidrug-resistant pathogenic bacteria presents a major current challenge, highlighting the urgent need for alternatives and sustainable biocontrol strategies. We aimed to isola...

Glad to have contributed to this study describing a novel Tequintavirus infecting Salmonella enterica serotype Tennessee.
My first involvement in bacteriophage research!
#phages #bacteriophage
link.springer.com/article/10.1...

26.11.2025 09:52 👍 1 🔁 0 💬 0 📌 0
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Glad to attend the @nf-co.re #Hackathon from Montpellier! Great collaboration, inspiring discussions, and lots of fun 🚀 #bioinformatics

24.03.2025 17:33 👍 4 🔁 2 💬 0 📌 0

My latest #Nextflow pipeline has just been published in JOSS 🎉

15.03.2025 19:45 👍 2 🔁 2 💬 0 📌 0
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Conda et le piège de la licence Anaconda - Bioinfo-fr.net Conda est appa­ru en 2012 et a été dis­tri­bué par Conti­nuum Ana­ly­tics, connue sous le nom d’Ana­con­da Inc depuis 2017. Conda est dis­tri­bué sous la licence MIT, l’une des licences open-source les plus per­mis­sives, per­met­tant aux uti­li­sa­teurs d’adopter, d’adapter et de par­ta­ger le logi­ciel presque sans res­tric­tions. Conda a été conçu pour gérer les envi­ron­ne­ments […]

📰 Vous n'avez rien compris au changement de licence Anaconda ? 🐍 On vous explique pourquoi et comment se mettre en règle :
https://bioinfo-fr.net/conda-et-le-piege-de-la-licence-anaconda
#bioinfofr #anaconda #conda

12.02.2025 09:02 👍 3 🔁 3 💬 0 📌 0

Super excited for the distributed nf-core hackathon! We've got 36+ local sites being organized in over 20 countries! Registration is now open!

04.02.2025 14:26 👍 4 🔁 2 💬 0 📌 0
list of banned keywords

list of banned keywords

🚨BREAKING. From a program officer at the National Science Foundation, a list of keywords that can cause a grant to be pulled. I will be sharing screenshots of these keywords along with a decision tree. Please share widely. This is a crisis for academic freedom & science.

04.02.2025 01:26 👍 27846 🔁 15745 💬 1272 📌 3656
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Registration to our #rstats Summer School RaukR 2025 Beyond The Basics is open! Don't miss the opportunity to elevate your R skillset! #r #datascience #bioinformatics #NBISweden @scilifelab.se

20.01.2025 13:48 👍 7 🔁 4 💬 2 📌 0
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Join us in welcoming the first cohort of 2025 Nextflow Ambassadors | Seqera It's time to welcome the new ambassadors who joined the Nextflow Ambassador Program for the 2025.1 semester.

I’m thrilled to join the first cohort of 2025 Nextflow Ambassadors! seqera.io/blog/welcome...
I'm still promoting #Nextflow and highlighting its incredible potential in #Bioinformatics, but with an Nextflow ambassador hat on now.It's good to be supported, thx @mribeirodantas.bsky.social @nextflow.io

21.01.2025 12:28 👍 8 🔁 1 💬 1 📌 0
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Bioinformatician in pipeline development - Uppsala University Bioinformatician in pipeline development, Department of Cell and Molecular Biology, Uppsala University

NBIS is seeking a #Nextflow pipeline developer ( permanent position ) in Uppsala, Sweden. www.uu.se/en/about-uu/.... Come join us and don't forget to include your Github/Gitlab/developer profile.

10.12.2024 08:32 👍 4 🔁 2 💬 0 📌 0
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29.11.2024 13:51 👍 279 🔁 43 💬 10 📌 1

#EDTA v2.2.2 is now available on #bioconda 🎉

26.11.2024 20:47 👍 0 🔁 0 💬 0 📌 0
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Day 2 of training to explore ANVIO with @tomdelmont.bsky.social at IRD Montpellier: an incredibly enriching experience! 🚀 #Bioinformatics #ANVIO

20.11.2024 18:50 👍 1 🔁 1 💬 0 📌 0
Home - Avoiding the Pitfalls of the Anaconda License Avoid conda licensing issues

Avoiding the pitfalls of Anaconda license changes: a practical guide

juke34.github.io/fix-anaconda...

13.11.2024 21:47 👍 0 🔁 2 💬 0 📌 0