Primer schemes

A versioned and schematised repository of tiling amplicon PCR primer scheme definitions (created with e.g. Primal Scheme) for pathogen sequencing, made with the objective of eliminating ambiguity in scheme naming and versioning in order to facilitate accurate analysis and reuse of amplicon sequence data.

Scheme specification

A scheme definition has three components:

1. A reference sequence (reference.fasta)
2. A seven column BED file of primer sequences & positions in reference coordinates (primer.bed)
3. A metadata file in YAML format adhering to this schema (info.yml)

Contributing new schemes

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.

Instructions

1. Choose an appropriate scheme name, e.g. schemename-v1, where v1 indicates the version of the scheme. Avoid including the organism name in the scheme name if possible.

2. Create a directory named schemename-v1 containing a text file info.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

3. Copy your scheme's BED file into this directory, naming it primer.bed

4. Copy your scheme's reference sequence into this directory, naming it reference.fasta

5. Optionally run primaschema build schemename-v1/ to create a finished scheme bundle

6. 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.

Tooling

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.

Documented schemes (24)

SARS-CoV-2 (22)

• 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

MPXV (1)

• yale-v3

NiV (1)

• nipah-v1