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NOTE THIS IS CURRENTLY BEING DEVELOPED PLEASE DO NOT USE.
Wrapper to basecall and demultiplex Sars-CoV-2 samples from ONT sequencing runs, then running the artic pipeline and finally assigning lineage with pangloin.
This wrapper script is intended for the use at the AMR lab at Stavanger University Hospital. It performs basecalling and demultiplexing of fast5 files from a nanopore sequencing run. It takes as input the fast5-folder from your sequencing run and will output a consensus.fasta sequence which you can use for further analyses (e.g. phylogeny, pangolin, etc.).
At the bottom of this README file you will find the commands for each step of the script if you want to run the analyses outside the pipeline.
Details
Computer requirements
Input files
Example Usage
Usage
Output
This script takes an ONT sequencing run, with or without barcodes, and performs basecalling and demultiplexing using the parameters described in https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html. It then runs the ARTIC pipeline via Nextflow (https://github.com/connor-lab/ncov2019-artic-nf) to produce consensus.fasta files for your Sars-CoV-2 genomes to be used in downstream analysis, such as pangolin lineage assignment or for upload to the GISAID database.