Docker Image for Artic Coronavirus Sequencing Pipeline
This contains a Dockerfile along with scripts for running the nCOV2019 sequencing pipeline developed by Artic: https://github.com/artic-network/artic-ncov2019
These tools are used for processing raw read data from an Oxford Nanopore sequencing machine. They are intended to be used by researchers, and this image contains additional files specifically for sequencing of the nCov-2019 virus.
This repo is currently being developed, but the core artic tools are present, so you can use them to run artic tools in a containerized environment.
docker pull skhan8/artic
You can now run artic tools using this image. For example,
docker run -it skhan8/artic artic basecaller
See the artic documentation for usage information.
Clone this repository and from the base folder run:
docker build -it artic .
Follow the instructions on this page to analyze your reads: https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html
Pull requests, issues, comments, and suggestions are welcome. Feel free to reach out to me directly as well via [email protected].