adding in include files for h5nx and h5n1 to capture recent cattle ou…

…tbreak sequences
nextstrain · Apr 17, 2024 · daf5151 · daf5151
1 parent 018f454
commit daf5151
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Showing 5 changed files with 210 additions and 6 deletions.
diff --git a/Snakefile b/Snakefile
@@ -1,15 +1,19 @@
-SUBTYPES = ["h5nx","h5n1","h9n2","h7n9"]
+SUBTYPES = ["h5nx","h5n1"]#["h5nx","h5n1","h9n2","h7n9"]
 SEGMENTS = ["pb2", "pb1", "pa", "ha","np", "na", "mp", "ns"]
 
 path_to_fauna = '../fauna'
 
 rule all:
     input:
-        auspice_json = expand("auspice/flu_avian_{subtype}_{segment}.json", subtype=SUBTYPES, segment=SEGMENTS)
+        #auspice_json = expand("auspice/flu_avian_{subtype}_{segment}.json", subtype=SUBTYPES, segment=SEGMENTS)
+        auspice_json = expand("auspice/avian-flu_{subtype}_{segment}.json", subtype=SUBTYPES, segment=SEGMENTS)
+        #sequences = expand("results/sequences_{subtype}_{segment}.fasta", subtype=SUBTYPES, segment=SEGMENTS),
+        #metadata = expand("results/metadata_{subtype}_{segment}.tsv", subtype=SUBTYPES, segment=SEGMENTS)
 
 rule files:
     params:
         dropped_strains = "config/dropped_strains_{subtype}.txt",
+        include_strains = "config/include_strains_{subtype}.txt",
         reference = "config/reference_{subtype}_{segment}.gb",
         colors = "config/colors_{subtype}.tsv",
         lat_longs = "config/lat_longs_{subtype}.tsv",
@@ -113,7 +117,8 @@ rule filter:
     input:
         sequences = rules.parse.output.sequences,
         metadata = metadata_by_wildcards,
-        exclude = files.dropped_strains
+        exclude = files.dropped_strains,
+        include = files.include_strains
     output:
         sequences = "results/filtered_{subtype}_{segment}.fasta"
     params:
@@ -129,6 +134,7 @@ rule filter:
             --sequences {input.sequences} \
             --metadata {input.metadata} \
             --exclude {input.exclude} \
+            --include {input.include}\
             --output {output.sequences} \
             --group-by {params.group_by} \
             --sequences-per-group {params.sequences_per_group} \
@@ -297,7 +303,7 @@ rule export:
         auspice_config = files.auspice_config,
         description = files.description
     output:
-        auspice_json = "auspice/flu_avian_{subtype}_{segment}.json"
+        auspice_json = "auspice/avian-flu_{subtype}_{segment}.json"
     shell:
         """
         augur export v2 \

diff --git a/clade-labeling/h5n1-clades.tsv b/clade-labeling/h5n1-clades.tsv
@@ -17811,3 +17811,85 @@ A/caspiantern/Washington/23024996001original/2023	2.3.4.4b
 A/Chicken/Netherlands/24001946006010/2024	EA-nonGsGD
 A/Tuftedduck/Netherlands/1/2023	EA-nonGsGD
 A/chicken/Iraq/KVCL016/2015	?
+          A/Ph/ST/44/2004	2.3.2
+A/chicken/Vietnam/Raho77232263/2023	2.3.2.1e
+A/duck/Vietnam/Raho723S2874/2023	2.3.2.1e
+A/duck/Vietnam/Raho723S2490/2023	2.3.2.1e
+A/Vietnam/KhanhhoaRV1005/2024	2.3.2.1e
+A/duck/Vietnam/Raho723S2875/2023	2.3.2.1e
+A/muteswan/Poland/MB055L2/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A045/2024	2.3.4.4b
+A/Fox/Bayern/i193/2023	2.3.4.4b
+A/feline/USA/24008764001original/2024	2.3.4.4b
+A/henharrier/Parnu/TA2126003/2021	2.3.4.4b
+A/chicken/CzechRepublic/3529/2024	2.3.4.4b
+A/domesticduck/Poland/H69T2/2024	2.3.4.4b
+A/goose/Bayern/wv196/2023	2.3.4.4b
+A/feline/USA/24009116005original/2024	2.3.4.4b
+A/muteswan/Poland/MB085N/2024	2.3.4.4b
+A/feline/USA/24009311006original/2024	2.3.4.4b
+A/chicken/CzechRepublic/47202/2024	2.3.4.4b
+A/chicken/Poland/H79T2/2024	2.3.4.4b
+A/muteswan/Poland/MB055L1/2024	2.3.4.4b
+A/dairycattle/Texas/24008749002v/2024	2.3.4.4b
+A/feline/USA/24009116004original/2024	2.3.4.4b
+A/domesticduck/Poland/H52T1K2/2024	2.3.4.4b
+A/chicken/CzechRepublic/35494/2024	2.3.4.4b
+A/chicken/CzechRepublic/31374/2024	2.3.4.4b
+A/feline/USA/24009116002original/2024	2.3.4.4b
+A/chicken/CzechRepublic/3744orig/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A031/2024	2.3.4.4b
+A/muteswan/Poland/MB055L4/2024	2.3.4.4b
+A/domesticduck/Poland/H57T1/2024	2.3.4.4b
+A/turkey/Poland/H40T2/2024	2.3.4.4b
+A/goose/Bayern/wv351/2023	2.3.4.4b
+A/domesticgoose/Poland/H49W/2024	2.3.4.4b
+A/turkey/Poland/H47T4/2024	2.3.4.4b
+A/turkey/Poland/H80T3/2024	2.3.4.4b
+A/Texas/37/2024	2.3.4.4b
+A/chicken/Poland/H45NM/2024	2.3.4.4b
+A/turkey/Poland/H75T1/2024	2.3.4.4b
+A/CommonBuzzard/GermanyBB/2024AI01490/2024	2.3.4.4b
+A/feline/USA/23037332001original/2023	2.3.4.4b
+A/feline/USA/24008850001original/2024	2.3.4.4b
+A/turkey/Poland/H68T2/2024	2.3.4.4b
+A/domesticduck/Poland/H66T1/2024	2.3.4.4b
+A/feline/USA/24009311004original/2024	2.3.4.4b
+A/turkey/Poland/H43T2/2024	2.3.4.4b
+A/chicken/CzechRepublic/354910/2024	2.3.4.4b
+A/chicken/CzechRepublic/34582/2024	2.3.4.4b
+A/NorthernFulmar/Netherlands/4/2024	2.3.4.4b
+A/largebilledcrow/Ishikawa/1702A010/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A044/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A033/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A032/2024	2.3.4.4b
+A/chicken/CzechRepublic/37442/2024	2.3.4.4b
+A/domesticduck/Poland/H60T4/2024	2.3.4.4b
+A/feline/USA/24008850002original/2024	2.3.4.4b
+A/Seagull/Parnu/TA21132845/2021	2.3.4.4b
+A/chicken/CzechRepublic/37443/2024	2.3.4.4b
+A/muteswan/Poland/MB070L1/2024	2.3.4.4b
+A/buzzard/Poland/MB098N/2024	2.3.4.4b
+A/chicken/CzechRepublic/31371/2024	2.3.4.4b
+A/turkey/Poland/H81T1/2024	2.3.4.4b
+A/domesticgoose/Poland/H48D1/2024	2.3.4.4b
+A/chicken/CzechRepublic/37441/2024	2.3.4.4b
+A/muteswan/CzechRepublic/4316/2024	2.3.4.4b
+A/buzzard/Poland/MB103N/2024	2.3.4.4b
+A/turkey/Poland/H63N/2024	2.3.4.4b
+A/chicken/CzechRepublic/35499/2024	2.3.4.4b
+A/largebilledcrow/Hokkaido/B114/2024	2.3.4.4b
+A/chicken/CzechRepublic/34583/2024	2.3.4.4b
+A/feline/USA/24008764002original/2024	2.3.4.4b
+A/eagle/Parnu/TA21118641/2021	2.3.4.4b
+A/turkey/Poland/H38T4/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A043/2024	2.3.4.4b
+A/chicken/CzechRepublic/34584/2024	2.3.4.4b
+A/chicken/CzechRepublic/31375/2024	2.3.4.4b
+A/Northernshoveler/Jeju/D60/2023	2.3.4.4b
+A/turkey/Poland/H543NM/2023	2.3.4.4b
+A/largebilledcrow/Osaka/2702A030/2024	2.3.4.4b
+A/CommonBuzzard/GermanyHH/2024AI01435/2024	EA-nonGsGD
+A/BarnacleGoose/GermanySH/2024AI01487/2024	EA-nonGsGD
+A/Dunlin/GermanySH/2024AI01484/2024	EA-nonGsGD
+A/Fox/Bayern/WS113/2022	?
diff --git a/clade-labeling/h5nx-clades.tsv b/clade-labeling/h5nx-clades.tsv
@@ -26824,3 +26824,95 @@ A/Eurasianteal/Netherlands/2/2023	EA-nonGsGD
 A/Mallard/Netherlands/12/2023	EA-nonGsGD
 A/mallard/Poland/P292w10/2023	EA-nonGsGD
 A/chicken/Iraq/KVCL016/2015	?
+          A/Ph/ST/44/2004	2.3.2
+A/Vietnam/KhanhhoaRV1005/2024	2.3.2.1e
+A/duck/Vietnam/Raho723S2875/2023	2.3.2.1e
+A/chicken/Vietnam/Raho77232263/2023	2.3.2.1e
+A/duck/Vietnam/Raho723S2490/2023	2.3.2.1e
+A/duck/Vietnam/Raho723S2874/2023	2.3.2.1e
+A/largebilledcrow/Hokkaido/B114/2024	2.3.4.4b
+A/feline/USA/24008850002original/2024	2.3.4.4b
+A/chicken/CzechRepublic/47202/2024	2.3.4.4b
+A/chicken/CzechRepublic/34584/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A031/2024	2.3.4.4b
+A/henharrier/Parnu/TA2126003/2021	2.3.4.4b
+A/chicken/CzechRepublic/31375/2024	2.3.4.4b
+A/chicken/CzechRepublic/31371/2024	2.3.4.4b
+A/chicken/CzechRepublic/35499/2024	2.3.4.4b
+A/turkey/Poland/H75T1/2024	2.3.4.4b
+A/largebilledcrow/Hokkaido/B112/2024	2.3.4.4b
+A/chicken/Poland/H45NM/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A032/2024	2.3.4.4b
+A/buzzard/Poland/MB098N/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A033/2024	2.3.4.4b
+A/goose/Bayern/wv351/2023	2.3.4.4b
+A/feline/USA/24009116002original/2024	2.3.4.4b
+A/NorthernFulmar/Netherlands/3/2024	2.3.4.4b
+A/chicken/CzechRepublic/31374/2024	2.3.4.4b
+A/feline/USA/24008850001original/2024	2.3.4.4b
+A/feline/USA/24009311006original/2024	2.3.4.4b
+A/domesticduck/Poland/H60T4/2024	2.3.4.4b
+A/chicken/CzechRepublic/354910/2024	2.3.4.4b
+A/domesticgoose/Poland/H48D1/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A045/2024	2.3.4.4b
+A/domesticgoose/Poland/H49W/2024	2.3.4.4b
+A/turkey/Poland/H63N/2024	2.3.4.4b
+A/Texas/37/2024	2.3.4.4b
+A/buzzard/Poland/MB103N/2024	2.3.4.4b
+A/largebilledcrow/Ishikawa/1702A010/2024	2.3.4.4b
+A/NorthernFulmar/Netherlands/1/2024	2.3.4.4b
+A/domesticduck/Poland/H57T1/2024	2.3.4.4b
+A/chicken/CzechRepublic/37443/2024	2.3.4.4b
+A/turkey/Poland/H43T2/2024	2.3.4.4b
+A/CommonBuzzard/GermanyBB/2024AI01490/2024	2.3.4.4b
+A/Fox/Bayern/i193/2023	2.3.4.4b
+A/turkey/Poland/H38T4/2024	2.3.4.4b
+A/chicken/CzechRepublic/34583/2024	2.3.4.4b
+A/feline/USA/24009311004original/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A030/2024	2.3.4.4b
+A/NorthernFulmar/Netherlands/4/2024	2.3.4.4b
+A/chicken/CzechRepublic/34582/2024	2.3.4.4b
+A/Seagull/Parnu/TA21132845/2021	2.3.4.4b
+A/turkey/Poland/H68T2/2024	2.3.4.4b
+A/feline/USA/24009116004original/2024	2.3.4.4b
+A/muteswan/Poland/MB055L2/2024	2.3.4.4b
+A/largebilledcrow/Hokkaido/B104/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A044/2024	2.3.4.4b
+A/goose/Bayern/wv196/2023	2.3.4.4b
+A/feline/USA/24009116005original/2024	2.3.4.4b
+A/muteswan/CzechRepublic/4316/2024	2.3.4.4b
+A/turkey/Poland/H543NM/2023	2.3.4.4b
+A/chicken/CzechRepublic/37441/2024	2.3.4.4b
+A/muteswan/Poland/MB055L1/2024	2.3.4.4b
+A/Sparrowhawk/England/133485/2024	2.3.4.4b
+A/chicken/Poland/H79T2/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A043/2024	2.3.4.4b
+A/muteswan/Poland/MB085N/2024	2.3.4.4b
+A/dairycattle/Texas/24008749002v/2024	2.3.4.4b
+A/feline/USA/23037332001original/2023	2.3.4.4b
+A/chicken/CzechRepublic/35494/2024	2.3.4.4b
+A/CommonBuzzard/England/133477/2024	2.3.4.4b
+A/chicken/CzechRepublic/3744orig/2024	2.3.4.4b
+A/feline/USA/24008764002original/2024	2.3.4.4b
+A/Northernshoveler/Jeju/D60/2023	2.3.4.4b
+A/Sparrowhawk/England/133522/2024	2.3.4.4b
+A/turkey/Poland/H81T1/2024	2.3.4.4b
+A/domesticduck/Poland/H52T1K2/2024	2.3.4.4b
+A/largebilledcrow/Hokkaido/B106/2024	2.3.4.4b
+A/chicken/CzechRepublic/3529/2024	2.3.4.4b
+A/eagle/Parnu/TA21118641/2021	2.3.4.4b
+A/muteswan/Poland/MB055L4/2024	2.3.4.4b
+A/feline/USA/24008764001original/2024	2.3.4.4b
+A/domesticduck/Poland/H69T2/2024	2.3.4.4b
+A/domesticduck/Poland/H66T1/2024	2.3.4.4b
+A/NorthernFulmar/Netherlands/2/2024	2.3.4.4b
+A/turkey/Poland/H47T4/2024	2.3.4.4b
+A/turkey/Poland/H80T3/2024	2.3.4.4b
+A/muteswan/Poland/MB070L1/2024	2.3.4.4b
+A/chicken/CzechRepublic/37442/2024	2.3.4.4b
+A/turkey/Poland/H40T2/2024	2.3.4.4b
+A/CommonBuzzard/GermanyHH/2024AI01435/2024	EA-nonGsGD
+A/RedKnot/GermanySH/2024AI01485/2024	EA-nonGsGD
+A/Dunlin/GermanySH/2024AI01484/2024	EA-nonGsGD
+A/BarnacleGoose/GermanySH/2024AI01487/2024	EA-nonGsGD
+A/Fox/Bayern/WS113/2022	?
diff --git a/config/include_strains_h5n1.txt b/config/include_strains_h5n1.txt
@@ -22,6 +22,18 @@ A/dairycattle/Texas/24008749004original/2024
 A/dairycattle/Texas/24008749006original/2024
 A/dairycattle/Texas/24008749007original/2024
 A/dairycattle/Texas/24008749005original/2024
+A/dairycattle/Texas/24008749002v/2024
 A/goat/Minnesota/24007234006original/2024
 A/goat/Minnesota/24007234009original/2024
-A/goat/Minnesota/24007234003original/2024
+A/goat/Minnesota/24007234003original/2024
+A/Texas/37/2024
+A/feline/USA/24009116005original/2024
+A/feline/USA/24008850001original/2024
+A/feline/USA/24009116004original/2024
+A/feline/USA/24009116002original/2024
+A/feline/USA/24008764001original/2024
+A/feline/USA/24009311006original/2024
+A/feline/USA/24008764002original/2024
+A/feline/USA/23037332001original/2023
+A/feline/USA/24008850002original/2024
+A/feline/USA/24009311004original/2024
diff --git a/config/include_strains_h5nx.txt b/config/include_strains_h5nx.txt
@@ -22,6 +22,18 @@ A/dairycattle/Texas/24008749004original/2024
 A/dairycattle/Texas/24008749006original/2024
 A/dairycattle/Texas/24008749007original/2024
 A/dairycattle/Texas/24008749005original/2024
+A/dairycattle/Texas/24008749002v/2024
 A/goat/Minnesota/24007234006original/2024
 A/goat/Minnesota/24007234009original/2024
-A/goat/Minnesota/24007234003original/2024
+A/goat/Minnesota/24007234003original/2024
+A/Texas/37/2024
+A/feline/USA/24009116005original/2024
+A/feline/USA/24008850001original/2024
+A/feline/USA/24009116004original/2024
+A/feline/USA/24009116002original/2024
+A/feline/USA/24008764001original/2024
+A/feline/USA/24009311006original/2024
+A/feline/USA/24008764002original/2024
+A/feline/USA/23037332001original/2023
+A/feline/USA/24008850002original/2024
+A/feline/USA/24009311004original/2024