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This is the pipeline that handles SARS-CoV-2 samples from the health sector in Region Midtjylland (Illumina PE)

KDHE Influenza A pipeline, built to take MinIon fastq files and produce clade analysis

Pipeline to generate consensus.fasta files and identify pangolin lineage and nextstrain clade of Sars-CoV-2 genomes from ONT sequencing

A template for building a custom Enterovirus Nextclade dataset

Complete pipeline that mirrors the manuscript: reference based assembly with depth masking, de novo checks, phylogeny with configurable models including ModelFinder, and targeted mutation analysis for G and F versus NC_038235.1 and NC_001781.1. Includes CI and environment files for easy setup.

Snakemake pipeline for creating a Nextclade dataset for Enterovirus D68