search

artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
Creative Commons Attribution 4.0 International
168 stars 166 forks source link

which version to use #52

Closed Shaokang123 closed 3 years ago

Shaokang123 commented 3 years ago

May I ask the difference of this pipeline and https://github.com/artic-network/fieldbioinformatics? It seems the later one updated more frequently, but this version is the one used in ARTIC network SOP https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html

Any suggestions? Thanks.

will-rowe commented 3 years ago

Hi @Shaokang123

That's a good question! In terms of differences between this repo and the one at fieldbioinformatics repo, the ARTIC pipeline itself is developed at the fieldbioinformatics repo - this is where the code lives and where you can download the development version or one of the releases.

This repository (artic-ncov2019) is more of a timestamped collection of resources for performing the ARTIC Network SOP. It is essentially just a conda environment which contains the ARTIC pipeline, as well as a few other resources (such as RAMPART).

The version of the ARTIC pipeline in the SOP will be periodically updated when we are happy with the latest pipeline changes. So in a few days/weeks we will update this repository to use the latest release of the ARTIC pipeline found at fieldbioinformatics repo.

As a side note - if you just want the latest ARTIC pipeline, you can now install direct from conda:

conda create -n artic-env
conda activate artic-env
conda install -c bioconda -c conda-forge artic
Shaokang123 commented 3 years ago

@will-rowe great, thanks for your reply. Appreciate your help.

Shaokang123 commented 3 years ago

Hi @will-rowe, if possible, may I ask for when will the SOP version of artic be updated?

will-rowe commented 3 years ago

Hopefully soon - just waiting on a code review from Nick before we make the next release and then update all the envs/SOPs across artic. Sorry I can't be more exact.

Shaokang123 commented 3 years ago

@will-rowe great, thanks so much, look forward to trying the new version