Update with new genomes

nextstrain · Mar 24, 2020 · 042790b · 042790b
1 parent a984e74
commit 042790b
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Showing 5 changed files with 180 additions and 30 deletions.
diff --git a/config/exclude.txt b/config/exclude.txt
@@ -39,10 +39,10 @@ Wuhan/HBCDC-HB-04/2019
 # Missing mutations
 Netherlands/Oisterwijk_1364072/2020
 Netherlands/Utrecht_1364066/2020
-Ireland/COR-20134/2020
 
 # Confusing phylogeography
 Netherlands/Rotterdam_1363790/2020
+Netherlands/NoordBrabant_5/2020
 
 # Missing precise date
 Netherlands/NoordBrabant_34/2020
@@ -60,6 +60,8 @@ Wuhan/IVDC-HB-envF54/2020
 Wuhan/WH02/2019
 Guangzhou/GZMU0016/2020
 Guangzhou/GZMU0047/2020
+HongKong/CUHK2/2020
+Wales/PHW06/2020
 
 # Excluding because seem to be too divergent - worth double checking
 Shandong/LY002/2020

diff --git a/config/lat_longs.tsv b/config/lat_longs.tsv
@@ -7,6 +7,7 @@ location	Berlicum	51.6789	5.4012
 location	Blaricum	52.2727	5.2481
 location	Boston	42.354750	-71.061299
 location	Brasilia	-15.814189	-47.875543
+location	Brisbane	-27.484246	153.026118
 location	Budapest	47.482728	19.084269
 location	California	36.357039	-119.690182
 location	Cardiff	51.476291	-3.178964
@@ -16,6 +17,7 @@ location	Chicago	41.858966	-87.637242
 location	Chongqing	29.858721	107.375623
 location	Chungcheongnam	36.685948	126.799198
 location	Clayton	-37.915200	145.127165
+location	Clark County	45.778260	-122.491540
 location	Coevorden	52.6614	6.7411
 location	Compiègne	49.408175	2.842839
 location	Contamines	45.820585	6.727730
@@ -32,6 +34,7 @@ location	Feira de Santana	-12.2598	-38.9675
 location	Foshan	23.018766	113.121428
 location	Garches	48.8461	2.1887
 location	Gold Coast	-28.019726	153.398160
+location	Grant County	47.163630	-119.524786
 location	Guangdong	23.615762	114.483257
 location	Guangzhou	23.123972	113.292889
 location	Gyeonggi	37.397957	127.380864
@@ -65,6 +68,7 @@ location	Loon	51.379197	5.443200
 location	Loon op zand	51.625527	5.070262
 location	Longjumeau	48.6931	2.2948
 location	Los Angeles	34.029267	-118.242865
+location	Manaus	-3.126424	-60.019807
 location	Melbourne	-37.839042	145.076343
 location	Milan	45.474	9.177
 location	Munich	48.155742	11.549380
@@ -87,6 +91,7 @@ location	Reims	49.253754	4.035860
 location	Rennes	48.1173	1.6778
 location	Riyadh	24.705304	46.738279
 location	Rio de Janeiro	-22.89445	-43.2099
+location	Rockhampton	-23.378823	150.509921
 location	Rome	41.881118	12.492817
 location	Rotterdam	51.9244	4.4777
 location	Rouen	49.4432	1.1000
@@ -112,6 +117,7 @@ location	Thanh Hoa	19.805359	105.784515
 location	Tianmen	30.6510	113.1556
 location	Tilburg	51.571419	5.052759
 location	Tokyo	35.683441	139.766131
+location	Umatilla County	45.648981	-118.720688
 location	Utrecht	52.0907	5.1214
 location	Valencia	39.337	-0.354
 location	Vila Velha	-20.3472	-40.2823
@@ -127,6 +133,7 @@ location	Zhuhai	22.271346	113.562879
 
 division	Aargau	47.420629	8.172097
 division	Aichi	35.067543	137.334061
+division	Amazonas State	-5.423668	-64.567836
 division	Andel	51.7851	5.0549
 division	Anhui	31.754331	117.211441
 division	Arizona	34.220707	-111.657462

diff --git a/config/ordering.tsv b/config/ordering.tsv
@@ -36,6 +36,8 @@ location	Singapore
 location	Gold Coast
 location	Sydney
 location	Melbourne
+location	Brisbane
+location	Rockhampton
 location	Clayton
 location	Auckland
 location	Riyadh
@@ -98,8 +100,9 @@ location	Helsinki
 location	Sao Paulo
 location	Brasilia
 location	Rio de Janeiro
-location	feira de santana
-location	vila velha
+location	Manaus
+location	Feira de Santana
+location	Vila Velha
 location	Mexico City
 location	King County
 location	Snohomish County
@@ -113,8 +116,11 @@ location	Los Angeles
 location	California
 location	San Francisco
 location	San Diego County
+location	Grant County
 location	Snohomish County
 location	King County
+location	Clark County
+location	Umatilla County
 location	Phoenix
 location	Chicago
 location	Illinois
@@ -252,6 +258,7 @@ division	Espirito Santo
 division	Bahia
 division	Rio de Janeiro
 division	Distrito Federal
+division	Amazonas State
 division	Panama City
 division	Mexico City
 division	USA
@@ -280,6 +287,7 @@ country	India
 country	Vietnam
 country	Cambodia
 country	Thailand
+country	Malaysia
 country	Singapore
 country	Australia
 country	New Zealand

diff --git a/config/weights.tsv b/config/weights.tsv
@@ -12,13 +12,17 @@ division_exposure	California	1.0
 division_exposure	Chongqing	10.0
 division_exposure	Chungcheongnam	1.0
 division_exposure	Comunitat Valenciana	1.0
+division_exposure	Connecticut	1.0
+division_exposure	Diamond Princess	1.0
+division_exposure	Distrito Federal	1.0
 division_exposure	Drenthe	1.0
 division_exposure	Dublin	1.0
 division_exposure	England	1.0
 division_exposure	Finland	1.0
 division_exposure	Flanders	1.0
 division_exposure	Flevoland	1.0
 division_exposure	Fujian	10.0
+division_exposure	Galicia	1.0
 division_exposure	Gelderland	1.0
 division_exposure	Geneva	1.0
 division_exposure	Grand Est	1.0
@@ -43,10 +47,12 @@ division_exposure	Kinshasa	1.0
 division_exposure	Kyoto	1.0
 division_exposure	Lapland	1.0
 division_exposure	Lazio	1.0
+division_exposure	Leuven	1.0
 division_exposure	Limburg	1.0
 division_exposure	Limerick	1.0
 division_exposure	Lombardy	20.0
 division_exposure	Luxembourg	1.0
+division_exposure	Madrid	1.0
 division_exposure	Massachusetts	1.0
 division_exposure	Mexico City	1.0
 division_exposure	Minnesota	1.0
@@ -58,6 +64,7 @@ division_exposure	Normandie	1.0
 division_exposure	North Brabant	1.0
 division_exposure	North Holland	1.0
 division_exposure	North Rhine Westphalia	1.0
+division_exposure	Northern Ireland	1.0
 division_exposure	Ontario	1.0
 division_exposure	Osaka	1.0
 division_exposure	Overijssel	1.0