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yykaya/README.md

👋 Hi, I'm Yasin Kaya

🎓 PhD Student in Plant Evolution & Bioinformatics at the Max Planck Institute for Plant Breeding Research (Hancock Lab) / University of Cologne

🧬 Researching pangenomes, structural variation, and adaptation in Arabidopsis thaliana & Arabis alpina

💻 Passionate about computational biology, population level pangenomics, and genome assembly pipelines

I’m currently working on

  • Comparative pangenome analysis of Arabidopsis thaliana and Arabis alpina from East Africa
  • Investigating structural variations and their role in adaptation
  • Developing bioinformatics tools for CNV/SV detection and pangenome integration

I’m currently learning

  • Nextflow pipeline optimization and containerization for genomics and transciptomics
  • Machine learning approaches for pangenomics
  • Advanced data analysis, visualization and pipeline development for genomics

📫 How to reach me

Programming & Tools

Programming:
•🐧 Linux •Python •R • C++ • Bash

Tools/Projects:

  • 🔗 PanHOG – A phylogeny-aware toolkit for classifying and annotating Hierarchical Orthologous Groups (HOGs) in pangenomic datasets
  • 🔗 Revelio – A lightweight C++ tool to identify cytosine contexts (CG/CHG/CHH) and assign sequence-based probabilities for methylation calling
  • 🔗 AraFusion – A pipeline for building and improving hybrid T2T genome assembly

📊 GitHub Stats

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  1. PanHOG PanHOG Public

    A phylogeny-aware toolkit for classifying and annotating Hierarchical Orthologous Groups (HOGs) in pangenomic datasets. It's a flexible command-line toolkit for classifying Orthofinder derived HOGs…

    Python 2

  2. AnkaPy AnkaPy Public

    Forked from DavidZihala/AnkaPy

    Python programming workshop for bioinformatics

    Jupyter Notebook

  3. abyss abyss Public

    Forked from bcgsc/abyss

    🔬 Assemble large genomes using short reads

    C++

  4. Dsuite Dsuite Public

    Forked from millanek/Dsuite

    Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species

    C++

  5. phylo-tutorials phylo-tutorials Public

    Forked from mmatschiner/tutorials

    Tutorials on phylogenetic and phylogenomic inference

    HTML

  6. modules modules Public

    Forked from nf-core/modules

    Repository to host tool-specific module files for the Nextflow DSL2 community!

    Nextflow