GenoFlow

🌾 First Chromosome-Scale Genome Assemblies of Tunisian Durum Wheat Landraces Chili & Mahmoudi - Assemblies & Data Now Public
We are thrilled to announce that the first -scale genome assemblies for the Tunisian durum wheat landraces and are now complete and publicly available!
These historically significant landraces, prized for high protein content (Chili, up to 17.3%) and drought/heat tolerance (Mahmoudi), now have reference-quality genomic resources, opening the door to marker-assisted breeding, comparative genomics, and pan-genome studies in North African germplasm.
🔬 Key Findings:
• Chromosome-scale assemblies with scaffold N50s of 845 Mbp (Chili) and 2,072 Mbp (Mahmoudi)
• Six independent validation layers confirming QV ~68 and BUSCO completeness >99%
• Independent wfmash validation: 98.6% mean alignment identity across 11,172 chromosome-to-reference alignments
• Comprehensive structural characterization: GC profiling, 24 rDNA loci, 9,456 structural variants, subgenome comparison (A vs B), and per-chromosome quality scoring
• Discovery of a putative 2B–3B homeologous fusion in Mahmoudi (4,710 Mbp Chr3B), a structural novelty in this ancient landrace
• Chromosome assignment achieved using k-mer sketching on consumer hardware (15 GB RAM), democratizing polyploid genome assembly
💻 PUBLIC DATA:
All assemblies, pseudomolecules, and supplementary datasets are openly deposited and freely accessible.
📄 First chromosome-scale genome assemblies and comprehensive structural characterization of Tunisian durum wheat (Triticum turgidum subsp. durum) landraces Chili and Mahmoudi
🔗 https://www.biorxiv.org/content/10.64898/2026.05.25.727644v2
💾 Zenodo — Assemblies & Data:
🔗 https://zenodo.org/records/20366290
📄 Unlocking Open-Access Genomic and Transcriptomic Data: The First Bioinformatic Exploitation of Tunisian Durum Wheat Landraces Chili and Mahmoudi
🔗 https://www.biorxiv.org/content/10.64898/2026.05.08.723814v2

This work builds on generated by the OpenDurumGPT consortium. Thank you for making this resource open to the community.

🌍 First shotgun metagenomics of diabetic foot ulcers from North Africa - now out in Frontiers in Microbiology
This was a genuine cross-border collaboration: Sabratha University, led patient recruitment and sample collection from 15 infected DFUs at Sabratha Teaching Hospital. , Tunisia contributed analytical expertise. supported the bioinformatics pipeline infrastructure.
On the data: The study combines new Libyan samples with (PRJNA506988, 25 non-infected DFUs) used as an ecological reference to understand depth-stratified microbial patterns and pre-infection resistance gene ecology. We are explicit that these two cohorts differ in infection status, geography, and clinical context, all between-cohort observations are descriptive, not comparative.
Key finding: First genomic evidence of the emerging multidrug-resistant clone Pseudomonas aeruginosa ST664 in a North African DFU , 220 virulence factors, 60 resistance genes, and 213 mobile genetic elements. Most DFU microbiome data comes from the US and Western Europe; this adds a much-needed North African perspective to the global conversation on antimicrobial stewardship in chronic wounds.

Frontiers | Metagenomic Characterization of Infected Diabetic Foot Ulcers in North Africa: Microbial Diversity, Virulome, and Resistome Profiling Diabetic foot ulcers (DFUs) are a major cause of lower-limb amputation worldwide. A better understanding of their microbiome can improve pathogen detection a...

🇹🇳 Celebrating Tunisian Scientific Innovation! 🌾
We are so proud to share the results of our latest study on Tunisian Durum Wheat! Our team of 4 young Tunisian researchers has been working hard to analyze, for the first time, the genomic data of our local landraces, Chili and Mahmoudi.
By using bioinformatics, we've explored how these ancient seeds naturally adapt to heat and drought. This is a step toward a more resilient future for our agriculture. 🧬✨

🙏 A Huge Thank You:
This work was made possible by the public datasets shared by the OpenDurumGPT consortium. Their commitment to Open Access is what allows local research to thrive and make an impact.

🌐 Explore our interactive webapp TuniTritica - available in two languages:
✨ Arabic version: TuniTritica 🇹🇳 https://nour0810.github.io/TuniTritica_AR/
✨ English version: TuniTritica 🌍 https://nour0810.github.io/TuniTritica/
📄 Read the full preprint:
bioRxiv - Full Paper https://www.biorxiv.org/content/10.64898/2026.05.08.723814v1
💻 Open-source code on GitHub:
github.com/nour0810/TuniTritica

🌾 من بذور أجدادنا... إلى مستقبل غذائنا العالمي:
باحثات تونسيات يحللن للمرة الأولى البيانات الجينية لقمحنا المحلي 🧬
بيانات جينومية نشرها باحثون تونسيون للعالم خلال الأيام الفارطة - باحثون آخرون عملوا على دراستها وتحليلها إجابةً للسؤال: ماذا تخبرنا هذه البيانات عن قمحنا؟ 🌱
لدينا في تونس كنزٌ زراعي حقيقي: القمح الصلب بصنفيه العريقين "الشيلي" و**"المحمودي"** - بذورٌ توارثناها عن أجدادنا، صمدت قرونًا أمام الجفاف والحرارة.
السؤال كان دائمًا: كيف تفعل ذلك؟ ما سرّها؟
في بادرة علمية قيّمة، قام فريق OpenDurumGPT بنشر البيانات الجينية الخام لصنفَي الشيلي والمحمودي مفتوحةً للمجتمع العلمي العالمي. فريقنا المتكوّن من أربع باحثات شابات تونسيات لبّى هذه الدعوة، وعملت على تحليل هذه البيانات ودراستها لأول مرة، باستخدام علم المعلوماتية الحيوية - وهو علم يقرأ "شيفرة الحياة" المخزّنة في كل بذرة - للكشف عن الجينات المرتبطة بقدرة هذا القمح التونسي الأصيل على تحمّل الحرارة والجفاف. 🔬

ماذا يعني هذا لك؟ 🍞
يعني أننا نُضيف لبنةً في بناء مستقبل فيه:
✅ قمحٌ لا يحتاج كميات ضخمة من الماء
✅ خبزٌ مضمونٌ حتى في سنوات الجفاف
✅ أمنٌ غذائي حقيقي لأجيالنا القادمة

🙏 شكر وتقدير:
هذا العمل تحقّق بفضل البيانات الخام المفتوحة التي وفّرها فريق OpenDurumGPT - لأن العلم حين يُشارَك، يتضاعف أثره.

🌐 جرّب نتائجنا بنفسك على أداتنا التفاعلية TuniTritica:
تصفّح الجينات، استكشف الكروموسومات، وشاهد كيف يختلف الشيلي عن المحمودي جينياً - بضغطة واحدة! 🖥️
✨ النسخة العربية: TuniTritica 🇹🇳 https://nour0810.github.io/TuniTritica_AR/
✨ النسخة الإنجليزية: TuniTritica 🌍https://nour0810.github.io/TuniTritica/

📄 اقرأ الدراسة كاملة:
bioRxiv - النص الكامل للورقة العلمية https://www.biorxiv.org/content/10.64898/2026.05.08.723814v1
💻 الكود مفتوح المصدر على GitHub:
github.com/nour0810/TuniTritica

#تونس #ابتكار

🎉 As GenoFlow completes its first year, we take a moment to reflect on what has already been achieved.

🚀 In just one year, GenoFlow has been actively engaged in capacity building and scientific collaboration across multiple regions. We organized and delivered bioinformatics workshops in Algeria 🇩🇿, Iraq 🇮🇶, and Libya 🇱🇾, in addition to several training sessions in Tunisia, both online and on-site.
The Tunisian workshops included 🇹🇳:
* Session conducted in collaboration with the IBRO project
* Two training sessions within the Innov’HER project, funded by UNESCO
* Two sessions organized with the Association Tunisienne des Professionnels en Biotechnologie et Environnement (ATPBE)
🌍 On the scientific side, GenoFlow established collaborations with academic and research institutions in Tunisia (University of Sfax, Tunis El Manar, Monastir, and Sousse), as well as with partners in Saudi Arabia 🇸🇦, Libya 🇱🇾, Belgium 🇧🇪, and France 🇫🇷.
🔬 Throughout this first year, GenoFlow contributed to projects in:
Metagenomics
- Genomics (bacterial and phage genomes)
- Sanger sequencing
- Biostatistics
- Scientific writing & publication support
📄 A major milestone of this inaugural year was the publication of the first scientific paper listing GenoFlow as an affiliation, alongside celebrating the publications of our collaborators. We also wish the best of luck to manuscripts currently under review, recently submitted, and those to be submitted very soon.
🙏 We sincerely thank all the researchers who trusted GenoFlow and continuously invited us to be part of their work. Through your projects, tasks, and scientific discussions, we learned a great deal. It is thanks to these collaborations that we are here today, celebrating these significant achievements together.
✨ This first year reflects GenoFlow’s commitment to rigorous science, knowledge transfer, and meaningful collaboration. We look forward to building even more in the years ahead.

🔬 [Metagenomics Workshop] CRSP Constantine 🇩🇿 x GenoFlow x BioTools

We had the privilege of participating in a metagenomics workshop hosted by CRSP Centre de Recherche en Sciences Pharmaceutiques - Constantine, in collaboration with GenoFlow and BioTools, and made possible thanks to the tremendous efforts of Dr. Abdellatif Guedou 🙏. His dedication and organization ensured that the event was both productive and welcoming.

The participants were engaged, curious, and motivated 💡, creating a warm, familial, and collaborative atmosphere 🤝 where we could all celebrate science together 🧬✨. Discussions were lively, hands-on sessions were interactive, and every moment reflected a shared passion for microbiome and metagenomic research.

At GenoFlow, we were proud to lead the practical sessions 🖥️, sharing our expertise in metagenomic workflows, bioinformatics pipelines, and data interpretation. We also learned a lot from the participants, whose enthusiasm and curiosity made the workshop truly constructive and rewarding.

We sincerely thank CRSP Constantine 💙 for their professionalism and kindness, all the organizers, and participants. A special thanks to Dr. Abdellatif Guedou 🙏, whose efforts were essential in making this workshop a successful, interactive, and joyful event 🎉.

This initiative reflects GenoFlow’s commitment 💻 to strengthening bioinformatics skills, fostering scientific collaboration, and promoting genomics-based innovation in the region.

📍 Constantine, Algeria
🧬 GenoFlow – Empowering precision through genomics





🔬 [ورشة الميتاجينوميات] 🇩🇿CRSP قسنطينة x GenoFlow x BioTools

تشرفنا بالمشاركة في ورشة الميتاجينوميات التي نظمها CRSP قسنطينة بالتعاون مع GenoFlow وBioTools، والتي أصبحت ممكنة بفضل الجهود الكبيرة لدكتور عبد اللطيف قدّو 🙏، الذي بفضل تفانيه وتنظيمه جعل الحدث مثمرًا وفي نفس الوقت دافئًا ومرحّبًا.

كان المشاركون متفاعلين، فضوليين، ومتحمسين 💡، مما خلق جوًا عائليًا وتعاونيًا 🤝 حيث تمكنا جميعًا من الاحتفال بالعلم معًا 🧬✨. كانت النقاشات حيوية والجلسات العملية تفاعلية، وعكست كل لحظة شغف المشاركين بمجال الميكروبيوم والميتاجينوميات.

في GenoFlow، كنا فخورين بـ قيادة الجلسات العملية 🖥️، ومشاركة خبرتنا في سير العمل الميتاجينومي، وتحليل البيانات، وتفسير النتائج. لقد تعلمنا الكثير أيضًا من المشاركين، الذين جعل حماسهم وفضولهم هذه الورشة تجربة تعليمية بنّاءة ومثمرة.

نتوجه بخالص الشكر إلى CRSP قسنطينة 💙 على احترافيتهم وكرمهم، وإلى جميع المنظمين والمشاركين على تعاونهم وحماسهم. وشكر خاص لدكتور عبد اللطيف قدّو 🙏 , فقد كانت جهوده أساسًا لجعل هذه الورشة ناجحة، تفاعلية، وممتعة 🎉.

تعكس هذه المبادرة التزام GenoFlow 💻 بـ تعزيز مهارات التحليل الحيوي المعلوماتي، وتشجيع التعاون العلمي، وتعزيز الابتكار المعتمد على الجينوميات في المنطقة.

📍 قسنطينة، الجزائر
🧬 GenoFlow – تمكين الدقة من خلال الجينوميات

🔬 [Metagenomics Workshop] GenoFlow x INNOVHER x UNESCO

GenoFlow had the pleasure of animating a 4-day workshop on metagenomics, organized within the framework of the Innov'her Science project, led by Dr. Sana Bardaa and supported by UNESCO .

The training covered key concepts and workflows in microbiome and metagenomic data analysis, combining theory with hands-on sessions.

We were pleased to welcome engaged participants from the de Sfax, Institut Pasteur de Tunis - معهد باستور تونس , and Centre de Biotechnologie de Borj Cedria - CBBC.

This initiative reflects our ongoing commitment to strengthening bioinformatics capacity and promoting genomics-based innovation across the region.

📍 Tunisia
🧬 GenoFlow – Empowering precision through genomics.

✨ Workshop Recap | Metagenomics with GenoFlow 🧬
📅 15–16 May 2025
📍 Faculty of Sciences of Sfax

Over the past two days, we had the pleasure of leading an intensive Metagenomics Workshop, hosted in collaboration with the Association Tunisienne des Professionnels en Biotechnologie et Environnement (ATPBE).

Through interactive sessions, we explored:
🔬 The fundamentals and applications of metagenomics
🧫 Bioinformatics tools and workflows
💡 Real-world case studies and hands-on data analysis

A special thank you to all the participants for their enthusiasm and curiosity, to ATPBE for the valuable partnership, and to the Faculty of Sciences of Sfax for hosting us.

🔗 Powered by GenoFlow – bringing genomics closer to practice.

🧠 GenoFlow at the 5th Edition of the Tunisian Neuroscience School
📍 Hammamet, Tunisia | April 27 – May 3, 2025
🎓 Theme: New Insights into the Cellular and Molecular Basis of Neurodegenerative Diseases

GenoFlow had the honor of participating in the 5th Edition of the Tunisian Neuroscience School, supported by IBRO (International Brain Research Organization). 🌍 IBRO is a global organization dedicated to promoting and advancing neuroscience research, particularly in developing countries. The organization fosters international collaboration and supports initiatives to train the next generation of neuroscientists. 🧑‍🔬👩‍🔬

During this event, GenoFlow presented a workshop on metagenomics 🧬, where we explored the role of microbial communities in neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s. Our workshop focused on how metagenomic tools can be applied to better understand the microbial influences on brain health and disease, bridging the fields of microbiome research and neuroscience. 🔬🧠

We are grateful for all the professors for their support 👏 and to all the participants for their engaging discussions and enthusiasm in this exciting area of research. 🌟

Genoflow at the Faculty of Sciences of Sfax: A Successful Metagenomics Workshop 🎓🔬

We are thrilled to have had the opportunity to collaborate with ATP-Be Association for a three-day workshop at the Faculty of Sciences of Sfax. The event focused on the latest advancements in metagenomics, offering participants an in-depth understanding of the field’s potential in microbiome research and its applications. 🌱🧬

Throughout the workshop, we presented Genoflow’s comprehensive approach to bioinformatics, highlighting the power of our platform in metagenomic data analysis. Participants learned valuable techniques for analyzing complex microbial communities and leveraging high-throughput sequencing data to uncover insights in microbial diversity, pathogenicity, and more. 📊💡

The collaboration with ATP-Be Association enabled us to bring together experts and researchers, fostering a dynamic learning environment. We are grateful for the engagement and enthusiasm shown by all attendees and look forward to continuing our mission of advancing research and knowledge in bioinformatics and genomics. 🚀🔍

Stay tuned for future training opportunities and workshops! 📅✨