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Achievements

Achievement: Pull Shark

Achievements

Achievement: Pull Shark

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@AMRmicrobiology

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jimmlucas/README.md

Hi, I'm Jimmy Lucas

Bioinformatics Engineer focused on reproducible omics workflows, scientific software, and scalable analysis

I work at the intersection of bioinformatics and engineering, building robust workflows for genomics, metagenomics, and microbial research. I enjoy turning complex analysis processes into reproducible, maintainable, and production-ready pipelines.

Main areas of work

  • Workflow engineering with Nextflow for reproducible omics pipelines
  • Genomics and metagenomics analysis in research and translational settings
  • Containerized and HPC-ready bioinformatics pipelines
  • Applied machine learning for sequencing workflow optimization and decision support
  • Statistical computing, data analysis, and visualization in Python and R

Featured projects

  • ESDP — ML framework for predicting optimal polishing rounds in ONT bacterial assemblies
  • WGS-Analysis-VariantCalling — Reproducible end-to-end Illumina bacterial WGS workflow
  • ONT_BACTERIAL_ANALYSIS — Reproducible end-to-end ONT bacterial genome analysis workflow

GitHub Stats

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  1. AMRmicrobiology/WGS-Analysis-VariantCalling AMRmicrobiology/WGS-Analysis-VariantCalling Public

    Nextflow pipeline for whole-genome sequencing (WGS) analysis and variant calling in bacterial genomes using Illumina data, supporting de novo assembly and reference-based analysis.

    Nextflow 6 2

  2. AMRmicrobiology/ONT_BACTERIAL_ANALYSIS AMRmicrobiology/ONT_BACTERIAL_ANALYSIS Public

    A scalable Nextflow pipeline for automated WGS analysis, optimized for Oxford Nanopore and hybrid ONT–Illumina assemblies in clinical microbiology research.

    Nextflow 2 1

  3. ESDP ESDP Public

    Decision-support framework for adaptive early stopping in Oxford Nanopore genome polishing.

    Python 1 1