new sampling schemes
@@ -109,12 +109,12 @@ subsampling:
# Focal samples for region
region:
group_by: "division year month"
- seq_per_group: 32
+ max_sequences: 2500
exclude: "--exclude-where 'region!={region}'"
# Contextual samples for region from the rest of the world
global:
group_by: "country year month"
- seq_per_group: 4
+ max_sequences: 1500
exclude: "--exclude-where 'region={region}'"
priorities:
type: "proximity"
@@ -122,9 +122,30 @@ subsampling:
# Custom subsampling logic for global region.
nextstrain_region_global:
- global:
+ africa:
+ group_by: "country year month"
+ max_sequences: 600
+ exclude: "--exclude-where 'region!=Africa'"
+ asia:
+ group_by: "country year month"
+ max_sequences: 700
+ exclude: "--exclude-where 'region!=Asia'"
+ europe:
+ group_by: "country year month"
+ max_sequences: 800
+ exclude: "--exclude-where 'region!=Europe'"
+ north_america:
+ group_by: "division year month"
+ max_sequences: 800
+ exclude: "--exclude-where 'region!=North America'"
+ south_america:
group_by: "country year month"
- seq_per_group: 16
+ max_sequences: 600
+ exclude: "--exclude-where 'region!=South America'"
+ oceania:
+ group_by: "division year month"
+ max_sequences: 500
+ exclude: "--exclude-where 'region!=Oceania'"
# Custom subsampling for regions like Europe where grouping by country
# is the smallest resolution requied
@@ -132,12 +153,12 @@ subsampling:
# Focal samples for region
region:
group_by: "country year month"
- seq_per_group: 44
+ max_sequences: 2500
exclude: "--exclude-where 'region!={region}'"
# Contextual samples for region from the rest of the world
global:
group_by: "country year month"
- seq_per_group: 5
+ max_sequences: 1500
exclude: "--exclude-where 'region={region}'"
priorities:
type: "proximity"
