search

nextstrain / WNV

the repository used to build West Nile Virus for nextstrain
https://nextstrain.org/WNV/NA
2 stars 0 forks source link

Decide on reasonable min-length filter #33

Open j23414 opened 4 weeks ago

j23414 commented 4 weeks ago

Context

Noticed some WA samples were being dropped due to the min-length filter (originally set to include at least 90% of the genome or 9800nt). We're considering dropping that lower to include more sequences as long as the phylogenetic tree looks reasonable.

The augur index of the WA sequences: wa_stats.txt

j23414 commented 3 weeks ago

Just documenting that min-length can be adjusted in the following locations:

Washington-specific

https://github.com/nextstrain/WNV/blob/ea9ec0e4b5295ad25b11c6532213054f2f1629d7/phylogenetic/build-configs/washington-state/config.yaml#L15-L20

global

https://github.com/nextstrain/WNV/blob/ea9ec0e4b5295ad25b11c6532213054f2f1629d7/phylogenetic/defaults/config.yaml#L67-L69