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ID records by genbank_accession
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j23414 committed Jan 12, 2024
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2 changes: 1 addition & 1 deletion phylogenetic/config/config_dengue.yaml
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strain_id_field: "accession"
strain_id_field: "genbank_accession"
display_strain_field: "strain"

filter:
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84 changes: 43 additions & 41 deletions phylogenetic/config/dropped_strains.txt
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Expand Up @@ -26,44 +26,46 @@ DENV2/TRINIDAD_AND_TOBAGO/NA/1953
DENV4/MALAYSIA/P215/1975
DENV4/MALAYSIA/P514/1975
DENV4/MALAYSIA/P731120/1973
D2Sab2015 # miscategorized
QML22 # miscategorized
DAK_Ar_A1247 # sylvatic
Dak_Ar_2039 # sylvatic
Dak_Ar_578 # sylvatic
DAK_Ar_510 # sylvatic
PM33974 # sylvatic
Dak_Ar_A2022 # sylvatic
Dak_Ar_141069 # sylvatic
Dak_Ar_141070 # sylvatic
Dak_Ar_D75505 # sylvatic
Dak_HD_10674 # sylvatic
Dak_Ar_D20761 # sylvatic
IBH11664 # sylvatic
IBH11208 # sylvatic
IBH11234 # sylvatic
P8_1407 # sylvatic
P75_514 # sylvatic
P73_1120 # sylvatic
P75_215 # sylvatic
DKD811 # sylvatic
ZS01/01 # metadata issue
Vero # cell line
MS13002673 # too divergent
MS11011405 # too divergent
V43257 # too divergent
KDC0574A2_06/02/2011 # too divergent
00178/03 # too divergent
00759/12 # too divergent
00988/11 # too divergent
01113/10 # too divergent
01224/04 # too divergent
01231/10 # too divergent
01488/09 # too divergent
01542/04 # too divergent
dev1 # too divergent
DKE_121 # too divergent
SENDAK_HD_10674 # sylvatic
DENV2_1_DAK_HD_76395 # sylvatic
DENV3/PUERTORICO/1963/PRS_228762_AC27 # too divergent
PR_6 # too divergent
KY923048 # D2Sab2015 # miscategorized
KX274130 # QML22 # miscategorized
EF105383 # DAK_Ar_A1247 # sylvatic
EF105382 # Dak_Ar_2039 # sylvatic
EF105380 # Dak_Ar_578 # sylvatic
EF105381 # DAK_Ar_510 # sylvatic
EF105378 # PM33974 # sylvatic
EF105386 # Dak_Ar_A2022 # sylvatic
EF105389 # Dak_Ar_141069 # sylvatic
EF105390 # Dak_Ar_141070 # sylvatic
EF457904 # Dak_Ar_D75505 # sylvatic
EF105384 # Dak_HD_10674 # sylvatic
EF105385 # Dak_Ar_D20761 # sylvatic
EF105388 # IBH11664 # sylvatic
EF105387 # IBH11208 # sylvatic
EU003591 # IBH11234 # sylvatic
EF105379 # P8_1407 # sylvatic
JF262779 # P75_514 # sylvatic
JF262780 # P73_1120 # sylvatic
EF457906 # P75_215 # sylvatic
FJ467493 # DKD811 # sylvatic
EF051521 # ZS01/01 # metadata issue
MT929160 # Vero # cell line
MH048676 # MS13002673 # too divergent
MH048674 # MS11011405 # too divergent
MT597439 # V43257 # too divergent
MN448607 # KDC0574A2_06/02/2011 # too divergent
ON046268 # 00178/03 # too divergent
ON046278 # 00759/12 # too divergent
ON046276 # 00988/11 # too divergent
ON046273 # 01113/10 # too divergent
ON046270 # 01224/04 # too divergent
ON046274 # 01231/10 # too divergent
ON046272 # 01488/09 # too divergent
ON046271 # 01542/04 # too divergent
MZ284953 # dev1 # too divergent
MZ215848 # DKE_121 # too divergent
MW946564 # SENDAK_HD_10674 # sylvatic
OK605757 # DENV2_1_DAK_HD_76395 # sylvatic
MW945427 # DENV3/PUERTORICO/1963/PRS_228762_AC27 # too divergent
OM258630 # PR_6 # too divergent
OP909734 # DENV2-16681-rcCap-NS1 # too divergent E gene
KR919820 # Brun2014 # highly divergent denv1
2 changes: 1 addition & 1 deletion phylogenetic/example_data/metadata_all.tsv
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strain virus accession date region country division city db segment authors url title journal paper_url
strain virus genbank_accession date region country division city db segment authors url title journal paper_url
DENV1/VIETNAM/BIDV1862/2008 dengue FJ410220 2008-XX-XX Southeast Asia Vietnam Vietnam Vietnam ? genome Alvarado et al. ? ? ? ?
DENV3/WALLIS_AND_FUTUNA/1404838/1989 dengue JQ920487 1989-08-14 ? Wallis And Futuna French Overseas Collectivity Wallis And Futuna ? genome Aubry et al. ? ? ? ?
DENV/BRAZIL/SJRP778/2013 dengue KT438585 2013-02-04 South America Brazil Brazil Brazil ? genome Araujo et al. ? ? ? ?
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2 changes: 1 addition & 1 deletion phylogenetic/example_data/metadata_denv1.tsv
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strain virus accession date region country division city db segment authors url title journal paper_url
strain virus genbank_accession date region country division city db segment authors url title journal paper_url
DENV1/INDIA/237/1962 dengue JF297572 1962-XX-XX South Asia India India India ? genome Cecilia et al. ? ? ? ?
DENV1/CHINA/RL6/2013 dengue KJ470727 2013-09-XX China China China China ? genome Guo et al. ? ? ? ?
DENV1/THAILAND/AILANDKPPKDV08491NC04528V0L/2007 dengue JQ993108 2007-XX-XX Southeast Asia Thailand Thailand Thailand ? genome Aldstadt et al. ? ? ? ?
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2 changes: 1 addition & 1 deletion phylogenetic/example_data/metadata_denv2.tsv
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strain virus accession date region country division city db segment authors url title journal paper_url
strain virus genbank_accession date region country division city db segment authors url title journal paper_url
DENV2/INDONESIA/MKS0084/2007 dengue KC762660 2007-11-21 Southeast Asia Indonesia Makassar Makassar ? genome Bifani et al. ? ? ? ?
DENV2/TAIWAN/71/2002 dengue EF016253 2002-XX-XX China Taiwan Taiwan Taiwan ? genome Ke et al. ? ? ? ?
DENV2/PAKISTAN/8D/2011 dengue JX042512 2011-XX-XX West Asia Pakistan Pakistan Pakistan ? genome Alvi et al. ? ? ? ?
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2 changes: 1 addition & 1 deletion phylogenetic/example_data/metadata_denv3.tsv
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strain virus accession date region country division city db segment authors url title journal paper_url
strain virus genbank_accession date region country division city db segment authors url title journal paper_url
DENV3/PUERTO_RICO/BIDV1615/2004 dengue FJ373302 2004-XX-XX North America Puerto Rico Puerto Rico Puerto Rico ? genome Alvarado et al. ? ? ? ?
DENV3/THAILAND/BIDV2323/2001 dengue FJ744734 2001-XX-XX Southeast Asia Thailand Kamphaeng Phet Kamphaeng Phet ? genome Alvarado et al. ? ? ? ?
DENV3/BANGLADESH/JACOB/NA dengue AY656673 ? South Asia Bangladesh Bangladesh Bangladesh ? genome Aaskov et al. ? ? ? ?
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2 changes: 1 addition & 1 deletion phylogenetic/example_data/metadata_denv4.tsv
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strain virus accession date region country division city db segment authors url title journal paper_url
strain virus genbank_accession date region country division city db segment authors url title journal paper_url
DENV4/ECUADOR/FSE2098/2006 dengue GQ139572 2006-XX-XX South America Ecuador Ecuador Ecuador ? genome Alava et al. ? ? ? ?
DENV4/BRAZIL/SJRP580/2012 dengue KP188562 2012-12-10 South America Brazil Brazil Brazil ? genome Araujo et al. ? ? ? ?
DENV4/BRAZIL/GUSP0670/2013 dengue KP704043 2013-03-17 South America Brazil Brazil Brazil ? genome Balarini et al. ? ? ? ?
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