Joep de Ligt's repositories
Advanced_Bioinformatics_StarterCode
Repo for teaching purposes in the Advanced Bioinformatics course, UMC Utrecht, 2016
PanGenomeGraph_microbe_paper
Paper writing for a first practical implementation of pangenome graph (pggb) for microbial genomics
Carpentries
Snippets relating the carpentries curriculum
Pangenome-Graphs-Workshop
This repository contains material to construct pangenome graphs for a small bacteria dataset detailing every step in the Nesi environment.
AMRdetection
Project to learn some Rust and do on the fly AMR detection
analysis-workflows
Open workflow definitions for genomic analysis from MGI at WUSM.
binding-site-predictor
Neural model to predict DNA binding sites of proteins
Deepbinner
a signal-level demultiplexer for Oxford Nanopore reads
diagnostics_exome_reporting
Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.
FAIR_genomics_models
Semantic models generated during a BYOD for CancerGenomics.nl
frontline_genomics_presentation
Our presentation on 'real-time' genomics for ESR Data Science Week 2020.
human_genomics_pipeline
A simple Snakemake workflow to process paired-end sequencing data (WGS) using bwa/GATK4.
Intro_Python
Description introduction to python
jdeligt.github.io
Presentations, home page, blog & useful code snippets
minimal-pathogen-agnostic-contextual-data-specification
An international minimal metadata standard for public health and One Health genomic surveillance.
python-novice-inflammation
Software Carpentry introduction to Python for novices using inflammation data.
sparqling-genomics
Ontologies, RDF-generators, and a web interface for querying it all.
Strain-specific-unmapped-reads
Scripts and pipelines for the analysis of strain-specific unmapped reads in 31 rat-strains
tb
TB runs with nextstrain-augur
Test-Carpentry-Python-2019
Workshop webpage