README.md

Primer sets

Dutch Primal 500-75

nCoV-nl-primal500-75.bed. These were extracted from the supplementary materials for [...], provided in primers/dutch_primal_amplicons.txt and preprocessed with the script primers/parse_nl_amplicons.py. Note that some of these primers were supplied with IUPAC ambiguous nucleotides which may present an issue with locating them in the reference sequence.

ARTIC-v3

Source: https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv

python parse_articv3_amplicons.py > nCoV-artic-v3.bed

ARTIC-v4

Source: https://github.com/artic-network/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V4/SARS-CoV-2.primer.bed

Midnight-1200

Source: https://docs.google.com/spreadsheets/d/1M5I_C56ZC8_2Ycgm9EFieVlVNqxsP7dXAnGoBZy3nDo/edit#gid=755704891

Target datasets

Nanopore

• PRJEB37966
• PRJEB37886 ARTIC v3(?) https://www.cogconsortium.uk/protocols/
• PRJEB38388 Dutch primers https://www.biorxiv.org/content/10.1101/2020.04.21.050633v1.supplementary-material
• PRJNA613958 https://peerj.com/articles/9255/
• PRJNA614995 https://peerj.com/articles/9255/
• PRJNA616147 ARTIC v1 primers
• PRJNA622817 https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html
• PRJNA627229 https://www.medrxiv.org/content/10.1101/2020.04.25.20079517v1.full.pdf
• PRJNA610248
• PRJNA614976 https://doi.org/10.1016/j.cell.2020.04.021
• PRJNA632678 https://doi.org/10.1128/MRA.00573-20
• PRJNA601630 https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30154-9/fulltext
• PRJNA608224 https://www.biorxiv.org/content/10.1101/2020.03.05.976167v1.full
• PRJNA608242
• PRJNA612578 https://www.biorxiv.org/content/biorxiv/early/2020/04/12/2020.04.09.034462.full.pdf
• PRJNA614504 https://europepmc.org/article/med/32676620
• PRJNA627286 https://onlinelibrary.wiley.com/doi/full/10.1002/jmv.26140

Illumina

• TODO