Duplication of Netherlands/Overijssel_2/2020

[pvanheus]

The virus name Netherlands/Overijssel_2/2020 is associated with both EPI_ISL_414550 and EPI_ISL_414460, with the former being dated later than the latter. I don't see an easy way to exclude one of what appear to be duplicates, but the duplicate name causes processing problems.

[trvrb]

Hi @pvanheus. We've just merged #59 that should fix this duplicates issue. After downloading from GISAID, run

./scripts/normalize_gisaid_fasta.sh data/gisaid_cov2020_sequences.fasta data/sequences.fasta

and then proceed with snakemake or nextstrain build, but let us know if this doesn't resolve things.

[pvanheus]

Thanks, I have my own Python script that does the same as that script.