Should pulling GPC sequences happen during the ingest or phylogenetic workflows?
If in the ingest, a reference might drop the 60pos gap. However, after discussion it looks like the Josiah reference is the longest (will not drop the gap). Therefore it was recommended to run Nextclade v3 against josiah and generate "results/gpc/sequences.fasta" and "results/gpc/metadata.tsv" files. This will still require augur align --extend alignment to keep the 60pos gap.
Planning documentation
Should pulling GPC sequences happen during the
ingestorphylogeneticworkflows?If in the
ingest, a reference might drop the 60pos gap. However, after discussion it looks like the Josiah reference is the longest (will not drop the gap). Therefore it was recommended to run Nextclade v3 against josiah and generate "results/gpc/sequences.fasta" and "results/gpc/metadata.tsv" files. This will still require augur align --extend alignment to keep the 60pos gap.