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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
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Basestack consensus

This pipeline is an implementation of the ARTIC network pipeline that is deployed in a Docker container that can be easily installed using the Basestack platform (https://github.com/jhuapl-bio/Basestack).

Normal usage

Install Basestack as described here: https://github.com/jhuapl-bio/Basestack and install the 'Consensus' module.

Development usage

The pipeline can be directly run, for development or other command line use, with the following commands:

  1. Download the latest version of the pipeline with:
docker pull jhuaplbio/basestack_consensus:latest
  1. Connect a MinION sequencing run folder to a container of that image:
docker container run \
  --rm \
  -it \
  -v /path/to/local/MinION/data:/opt/basestack_consensus/sequencing_runs/example-run \
  jhuaplbio/basestack_consensus:latest \
  bash
  1. Within the container, run the pipeline on the MinION run folder: 
    artic-module1-barcode-demux.sh -i /opt/basestack_consensus/sequencing_runs/example-run

misc

To run a dev process on the image on a mounted path, do:

docker container run -it --rm -v $ROOT_DATA_PATH:/opt/run-data -v $PWD:/opt/basestack_consensus/code/ncov --name basestack_consensus jhuaplbio/basestack_consensus

where $ROOT_DATA_PATH is the path to the run directory. The pipeline will output to artic-pipeline in that folder