Update SARS-CoV-2 primer schemes with V4

[szufan]

Could you update the SARS-CoV-2/nCoV-2019 schemes to include V4?

https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V4

Many thanks, Sara

[nickloman]

Sorry Sara, what do you mean exactly?

[szufan]

Hi Nick, so I've installed artic from source via fieldbioinformatics repo (as opposed to artic-ncov-2019, not sure if that makes a difference). schemes_manifest.json contains V1-3, but not V4.

Here's my output from artic-tools get_scheme nCoV-2019 --schemeVersion 4

[10:19:48] [artic-tools::get_scheme] starting primer scheme downloader
[10:19:48] [artic-tools::get_scheme]    requested scheme:       nCoV-2019
[10:19:48] [artic-tools::get_scheme]    requested version:      4
[10:19:48] [artic-tools::get_scheme] fetching manifest file
[10:19:48] [artic-tools::get_scheme]    ARTIC manifest URL:     https://raw.githubusercontent.com/artic-network/primer-schemes/master/schemes_manifest.json
[10:19:48] [artic-tools::get_scheme]    ARTIC repository DOI:   10.5281/zenodo.4004423
[10:19:48] [artic-tools::get_scheme] finding primer scheme
[10:19:48] [artic-tools::get_scheme]    found requested scheme: sars-cov-2 (using alias nCoV-2019)
[10:19:48] [artic-tools::get_scheme]    requested version not found (v4), using latest version instead (v3)
[10:19:48] [artic-tools::get_scheme] downloading primer scheme
[10:19:48] [artic-tools::get_scheme]    saving primers to:      nCoV-2019.v3.primer.bed
[10:19:48] [artic-tools::get_scheme]    saving reference to:    nCoV-2019.v3.reference.fasta
[10:19:48] [artic-tools::get_scheme] comparing checksums
[10:19:48] [artic-tools::get_scheme]    sha256 for primers:     6e98d7d5d1c6edac8ef0bac70d698e0828ae42bafe8f3bda0a6257d00ce414b5
[10:19:48] [artic-tools::get_scheme]    sha256 for reference:   b09a4a3d6824dc4a9f3a17d480f3335f73cb1507897f6dad0de871e8f00d8637

[nickloman]

Ah OK! Yes, needs adding to the scheme.json file - will sort.

[szufan]

Thanks!