quokka

QUality Of Known Klusters Assessed

To do

check SNPs for each lineage, are there some sequences that have missing sites at what otherwise be defining SNPs
are there any obvious sequences that look like they belong in different lineages
check ambiguity content
check monophyly within a tree (figtree2, usher and nextclade), or within updown-topranking gofasta
check decision tree for each lineage, see if any conflicting decisions or any that dont seem to fit
get 95% consensus of a lineage, check if outliers and remove
Do all records on pango-designation match the gisaid metadata file? If not which ones and why (e.g. misspellings, or wrong year etc).
Do all lineages have records?
Are there sequences designated a lineage that scorpio disagrees with?
Are there sequences that are in the metadata that scorpio calls that we should
Do all sequences in a certain lineage have the set of mutations that they should have? Are there ones that really stick out?
Primer sites/ problematic sites check
Designate identical sequences routinely
Input fasta file, output ambiguity content