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:

• 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:

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.
• 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: 25.08.2020

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 5 in the BED spec is an int for score, whereas here we are using it to denote primerPool.

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;