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;