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bbalog87/README.md

Hi there 👋

Welcome, I am Julien!

  • I'm a trained bioinformatician and currently a Senior Bioinformatics Scientist at the Bernard-Nocht Institute (BNI) for Tropical Medicine
  • I integrate well-established NGS technologies for microbial & animal genome assembly and annotation;
  • I use HPC for large scale data processing;
  • I am R enthiast, which I primarily leverage for data cleaning, wrangling and visualization in the tidyverse ecosystem;
  • I use BASH and python for scripting pipeline and reformatting data;
  • Both Conda and Nextflow are good friends of mine;
  • I leverage BASH and python for developing workflows;
  • I advocate for reproducible research and open science by making my workflows and pipelines as transparent and reprocdicele as posible.

Pinned Loading

  1. compleasm-batch-wrapper compleasm-batch-wrapper Public

    Compleasm Batch Runner for Genome Assembly Completeness Assessment (BUSCO)

    Shell

  2. fluoroquinolone-AMR-campylobacter fluoroquinolone-AMR-campylobacter Public

    Scripts, workflows, and results for analyzing quinolone and fluoroquinolone resistance in global Campylobacter isolates

    R

  3. amr-ngs-pipeline amr-ngs-pipeline Public

    A Nextflow pipeline for NGS antimicrobial resistance profiling. From raw NGS FASTQ to rendered AMR profiles

    Shell

  4. taxon_aware_amr taxon_aware_amr Public

    Taxon-aware AMR and virulence detection for heterogeneous one health surveillance inputs.

    Python