🚨 Follow development of the version 1.0 specification in the v1a
branch of primaschema
. Schemes in this repository will be migrated to the v1 specification first in branch v1a
and then main
.
A versioned and schematised repository of tiling amplicon primer scheme definitions (created with e.g. Primal Scheme) for pathogen sequencing, made with the objective of eliminating ambiguity in scheme naming and versioning and maximising the findability, accessibility, interoperability and reusability (FAIRness) of primer scheme definitions and associated sequencing data.
A scheme definition has three components:
- A reference sequence (
reference.fasta
) - A seven column BED file of primer sequences & positions in reference coordinates (
primer.bed
) - A metadata file in YAML format adhering to this schema (
info.yml
)
We welcome contributions of new primer schemes! We're working to make this process easier, but in the meantime please either follow the instructions below and create a pull request, or else open a GitHub issue attaching or linking to a BED file so that we can help.
-
Choose an appropriate scheme name, e.g.
schemename-v1
, wherev1
indicates the version of the scheme. Avoid including the organism name in the scheme name if possible. -
Create a directory named
schemename-v1
containing a text fileinfo.yml
containing:schema_version: 0.9.0 name: schemename-v1 organism: sars-cov-2 developers: - person_name: Jane Doe orcid: 1234-5678-9876-5432 amplicon_size: 1200 repository_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/schemename/v1
-
Copy your scheme's BED file into this directory, naming it
primer.bed
-
Copy your scheme's reference sequence into this directory, naming it
reference.fasta
-
Optionally run
primaschema build schemename-v1/
to create a finished scheme bundle -
Either open a pull request adding your scheme directory (e.g. inside
sars-cov-2/schemename/v1
), or else open a GitHub issue attaching a zip file containing your scheme.
The companion tool Primaschema can be used to validate scheme definitions and automatically checks and updates this repository via GitHub Actions. Primaschema adds primer and reference sequence checksums to info.yml
at build time to help catch identical primer schemes. A six column scheme.bed file is also generated at build time for legacy compatibility.
artic-v1
artic-v2
artic-v3
artic-v4
artic-v4.1
artic-v5.0.0_400
artic-v5.1.0_400
artic-v5.2.0_1200
artic-v5.2.0_400
artic-v5.3.2_400
eden-v1
midnight-bccdc-v1
midnight-bccdc-v2
midnight-bccdc-v3
midnight-bccdc-v4
midnight-ont-v3
midnight-v1
midnight-v2
varskip-vsl1a
varskip-vss1a
varskip-vss2a
varskip-vss2b
yale-v3
nipah-v1