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.
GNU General Public License v3.0
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ONT depth threshold showing intermittent errors #32
Depth threshold should always be numeric and always be greater or equal to 20.
Threshold value is grabbed from
postfilt_all.txtoutput file in module 5 in two places.Seems to be as a result of some stochastic process in creating
postfilt_all.txtwith rows that either contain a value (e.g.20) or a period.