Primer schemes for real-time genome epidemiology
The primer schemes in this repository were built using Primal Scheme and are available for the following viruses:
- Monkeypox virus (mpxv-2022)
Within each virus directory, there are versioned sub-directories which each contain a versioned scheme for that virus.
The following files are available per scheme version:
| file extension | about |
|---|---|
.primer.bed |
The coordinates of each primer in the scheme |
.insert.bed |
The coordinates of the expected amplicons that the scheme produces (excluding primers) |
.reference.fasta |
The sequence of the reference genome used for the scheme |
.tsv |
Details on each primer in the scheme (name, sequence, length, GC, TM) |
For more information visit the ARTIC network website.
- There may be some additional files in the scheme directories - these are either deprecated and left for backward compatibility (e.g.
scheme.bed), or are created by Primal Scheme check here for more info. - The schemes are in BED format, which is a 0-based, half-open format. This means that reference sequence position counting starts at 0 and the chromEnd is not included in the primer sequence.
The .scheme.bed file has the following columns:
| column | name | type | description |
|---|---|---|---|
| 1 | chrom | string | primer reference sequence |
| 2 | chromStart | int | starting position of the primer in the reference sequence |
| 3 | chomEnd | int | ending position of the primer in the reference sequence |
| 4 | name | string | primer name |
| 5 | primerPool | int | primer pool* |
| 6 | strand | string (+/-) | primer direction |
* column 5 in the BED spec is an int for score, whereas here we are using it to denote primerPool.