This Snakemake workflow performs basecalling for Nanopore sequencing runs. It was specifically testet for output of the MinION Mk1B.
The workflow basically uses ONT Guppy to perform the basecalling and demultiplexing. In addition, it assigns sample names to the output according to the aliases for the barcodes in the sample sheet. It runs some QC, e.g. pycoQC, NanoPlot, as well as some custom scripts.
The workflow uses the output folder from MinKNOW as input, i.e. fast5 files.
In order to start the workflow the user has to:
- provide a sample sheet file (e.g.
sample_sheets/sample_sheet.csv) - configure the Snakemake config file (
config/config.yaml).
The workflow can be started by running the run.sh on the shell.
Mohren et al. (2024). Advancing molecular, phenotypic and mechanistic insights of FGF14 pathogenic expansions (SCA27B). in prep.