A script that does live read mapping of nanopore sequencing. While this can be run standalone, it's main use is to built in as part of other pipelines, see https://github.com/KMA-Aarhus/pappenheim
This is built for bacterial and viral genomes and is not suitable for larger genomes.
Also note that this requires unix exclusive gnome-terminal and browsersync software. While the scripts can be run on windows or macOS, the live updates will not work
- conda installation (mamba recommended
- browser-sync
- samplesheet linking barcodes to samples
- one or more references
mamba env create -f covermon.yaml
To run call the script with the following inputs in the following order: (1) samplesheet (2) path to run directory (3) path to reference or reference directory (4) threshold for minimum coverage (5) maximum depth displayed in plot Optional (6) a region file can be specified if all samples use the same reference genome.
mamba env create -f covermon.yaml