primerschemes

Central machine-readable repo for newly generated PrimerSchemes and PrimalPanels

For a user-navigable version please go here

Quick Start

Each version of a primerscheme has three parts; {schemename}/{ampliconsize}/{version}, which when combined form the scheme's unique identifier.

For a scheme to be added to the repo it requires three essential files.

• primer.bed: Contains the primer information.
• reference.fasta: Contains the reference genomes.
• info.json: Contains key metadata for the scheme.

The primal-page create command will generate the info.json and parses a bed file and a fasta file into primer.bed and reference.fasta

Additional files are copied into the schemes work directory.

See primal-page for more details.

What does part each mean?

schemename

The family of scheme.

The naming format is flexible, but we encourage the form of {group}-{target}. For example artic-sars-cov2

• Follow good scientific naming practices. No places. No vague names (sar2)

ampliconsize

The amplicon size of the scheme in nucleotides. PCR products typically are ± 10%. Shorter schemes (400bp) generally are more sensitive, down to Ct 35+, compared to larger schemes (2000bp), down to Ct 30.

version

The version of the scheme. This follows the format of vz.y.x-abc. Selecting the correct version is vital for wet lab work and bioinformatic analysis.

• z: represents a total resigned of a scheme.

• y: represents a change in primers to an existing scheme. Ie adding spike in primers to account for new mutations.

• x: represents a change in the primer concentration used. No change to the primer sequences.

• -abc: an optional suffix to represent a scheme being remapped to a new reference genome. No changes to the primer sequences or concentration.

Examples

v2.0.0 is an entirely different scheme to v1.0.0.

v1.0.0 has two additional primers added to account for a new mutation. The new scheme would be v1.1.0

v1.1.0 has primer concentrations changed to improve even coverage of amplicons. The new scheme would be v1.1.1

v1.0.0 has identical primers (sequence and concentration) to v1.0.0-alpha. However, the primers will now be mapped to the alpha reference genome.