Repositories

Research code, bioinformatics pipelines, and reproducible workflows.

🧬 Research Repositories

This page provides an overview of code repositories, pipelines, and computational resources I maintain or actively develop. My repositories emphasize reproducibility, scalability, and clarity, with workflows designed for HPC environments and real-world biological datasets.

Most projects are hosted on GitHub:

🔗 GitHub: https://github.com/jojyjohn28

🔗 Blog for more details : https://jojyjohn28.github.io/blog/

🧪 Amplicon Analysis

🔗 https://github.com/jojyjohn28/AmpliconWeek_2025

A structured, day-by-day workflow for amplicon sequencing analysis, developed as both a training resource and a reproducible analysis guide.

Focus areas:

  • QIIME2-based amplicon processing
  • Diversity analysis and visualization
  • Ecological interpretation of ASVs
  • Best practices for reproducible workflows

🌊 Size_Fractionated_Microbiome_Analysis**

🔗 https://github.com/jojyjohn28/Size_Fractionated_Microbiome_Analysis

A comprehensive analysis framework for free-living and particle-associated microbial communities, integrating metagenomics and metatranscriptomics.

Focus areas:

  • Read-based taxonomic and functional profiling
  • DNA–RNA comparisons (total vs active communities)
  • Resource partitioning and substrate uptake
  • Functional redundancy (FRed) analysis
  • Co-occurrence and ecological interpretation

🧬 Genome-Resolved Metagenomics

🔗 https://github.com/jojyjohn28/semibin2-soil-mag-workflow

A Snakemake-based workflow for SemiBin2-assisted MAG recovery, optimized for soil and complex environmental metagenomes.

Focus areas:

  • Co-assembly and binning strategies
  • Semi-supervised MAG recovery
  • Genome quality assessment
  • Scalable execution on HPC systems

Across all repositories, I emphasize:

  • Reproducibility over one-off scripts
  • Clear documentation and modular design
  • Compatibility with HPC environments (SLURM)
  • Teaching workflows that users can reproduce and troubleshoot independently

These repositories are used in research projects, student mentoring, and collaborative studies.

📌 Notes

  • Repositories may changes as the work progress.!