Artic-ncov2019 primer scheme V5.3.2 about covid-19-signal HOT 3 CLOSED

Hi,

Yes, you can use the primer scheme from another pipeline if you desire. To do so would require the .bed file defining the scheme. This .bed will be used when invoking ivar trim.

Within your config.yaml file, you would substitute the following parameter with the corresponding path to the .bed file on your system.

# Path from snakemake dir to .bed file defining amplicon primer scheme
scheme_bed: 'resources/primer_schemes/artic_v3/nCoV-2019.bed'

The path in the example is simply the default and can be changed with any of the scheme we provide (including some from artic-network) or your own.

Hope this helps.

from covid-19-signal.

You're welcome! Feel free to re-open this issue if you come across problems regarding the primer schemes.

from covid-19-signal.

Thank you so much for your confirmation on this.

from covid-19-signal.