This repository is a Dockerized pipeline for creating consensus viral genomes from Oxford Nanopore data. This pipeline leverages the ARTIC Network bioinformatics pipeline and couples many annotation and reporting tools, resulting in an automatically generated PDF report. The pipeline is built to be deployed in the Basestack platform (https://github.com/jhuapl-bio/Basestack) so that anyone, regardless of bioinformatics expertise, can run it and make use of its automated consensus genomes and reports.
Is it possible to continue pipeline despite some misnamed or extra barcodes module?
For instance if 12 barcodes are provided in the manifest but only 9 are available in the data. This is mainly concerning unsuccessful or poor runs where a report is still desired.
Is it possible to continue pipeline despite some misnamed or extra barcodes module?
For instance if 12 barcodes are provided in the manifest but only 9 are available in the data. This is mainly concerning unsuccessful or poor runs where a report is still desired.