ARTIC pipeline¶
In this part of the tutorial, we are using the ARTIC pipeline to generate a consensus sequence from the Wuhan reference and our amplicon data.
The complete ARTIC bioinformatics SOP can be found here: https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html
Since we already have basecalled and demultiplexed data, we start with the step “Read filtering”.
The ARTIC pipeline is installed in a conda environment which we need to activate with:
conda activate artic-ncov2019
When activated, your shell looks like this:
(artic-ncov2019) ubuntu@nanopore-course-2020:~$
This indicates, that the artic-ncov2019 environment is active. When no environment is active, your shell indicates that with “(base)” at the start of the line like this:
(base) ubuntu@nanopore-course-2020:~$
This is for example the case, when you open a new shell. You can also deactivate the active conda environment with:
conda deactivate
Always make sure the artic-ncov2019 environment is active in this part of the tutorial.