emilieegholmbruun/frontline_metagenomics

This repository provides the underlying code for the results published in"Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics ", which can be accessed here: xxx # Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics This repository contains the underlying code used in the paper: "Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics " by Jensen and Nzoyikorera et al. (2026). # HPC-based analysis ## Host removal - `remove_host.sh` - `run_remove_host.sh` ## Metagenomic read-alignment to database - `snake.kma_rugombo_old_new.py` - `snake.kma_rugombo.py` - `snake.kma_cibitoke.py` - `snake.kma_rutana.py` - `kma_VFDB.sh` ## Single isolates - `snake.flye.py` - `snake.single_isolates_metabat2.py`