Assumed ncov-2019 primer reference

jhuapl-bio / basestack_consensus

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

2 stars 2 forks source link

Assumed ncov-2019 primer reference #29

Closed Merritt-Brian closed 3 years ago

Merritt-Brian commented 3 years ago

Issue: The pipeline assumes that the prefix-names for primer scheme files begin as ncov-2019.

Example using the ZaireEbola primer schemes from artic network:


.
.
.
Copyright (C) 2019 Genome Research Ltd.

2021-02-19T19:56:51.513Z [info]: [2021-02-19 19:56:51] SAMPLE MDHP-0065---_NB11: Reference fasta: /root/idies/workspace/covid19/code/artic-ncov2019/primer_schemes/ZaireEbola/V2/nCoV-2019.reference.fasta

.
.
.