primer-schemes
Primer schemes for real-time genome epidemiology
About
The primer schemes in this repository were built using Primal Scheme and are available for the following viruses:
- Ebola
- Nipah
- SARS-CoV-2 (nCoV-2019)
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.
Notes
- 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.
- All the schemes within this repository can be downloaded using artic-tools (e.g.
artic-tools get_scheme ebola --schemeVersion 2) - The SARS-CoV-2 directory is an alias to the original nCoV-2019 directory, left for backwards compatibility
Updated scheme file format
updated: 25.08.2020
changes
With the major version bump to Primal Scheme, primer schemes are now output to *.primer.bed files.
These new files aren't much different to the old *.scheme.bed files and the same information is contained within, but they now conform to the BED standard.
The new format 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.
commands
The liftover.py script was used to create a *.primer.bed file for each *.scheme.bed file, within each scheme directory in this repository.
The validate_scheme command from artic-tools was used to validate each *.primer.bed and also to create the *.insert.bed file which is produced by recent versions of Primal Scheme.
The following commands where used:
for i in */V*/*.scheme.bed;
do
basename=${i%%.scheme.bed}
scripts/liftover.py -i $i -o ${basename}.primer.bed;
artic-tools validate_scheme ${basename}.primer.bed --outputInserts ${basename}.insert.bed
done;