Skip to content

Commit

Permalink
Use accession column as ID column
Browse files Browse the repository at this point in the history 
The same samples are used for example data as were previously used,
but now they have been pulled from the ingest output.
Ambiguous dates were manually fixed in the example data for samples
JN635406.1, JN635408.1, and EF565859.1, based on dates found here:
https://github.com/nextstrain/fauna/blob/master/source-data/measles_date_fix.tsv
  • Loading branch information
@kimandrews
kimandrews committed Mar 9, 2024
1 parent 71a2744 commit e2d56c7
Show file tree
Hide file tree
Showing 7 changed files with 5,176 additions and 5,165 deletions.
4 changes: 4 additions & 0 deletions phylogenetic/defaults/config.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,13 @@ filter:
sequences_per_group: 20
min_date: 1950
min_length: 5000
strain_id: "accession"
refine:
coalescent: "opt"
date_inference: "marginal"
clock_filter_iqd: 4
strain_id: "accession"
ancestral:
inference: "joint"
export:
strain_id: "accession"
4 changes: 2 additions & 2 deletions phylogenetic/defaults/dropped_strains.txt
View file
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
temara.MOR/24.03
Mvs/Toulon.FRA/08.07
HM562901.1 # temara.MOR/24.03
HM562900.1 # Mvs/Toulon.FRA/08.07
42 changes: 21 additions & 21 deletions phylogenetic/example_data/metadata.tsv
View file
Original file line number Diff line number Diff line change
@@ -1,21 +1,21 @@
strain virus accession date region country division city db segment authors url title journal paper_url
Arizona.USA/11.08/2 measles JN635406 2008-03-11 North America Usa Usa Usa genbank genome Kirkness et al https://www.ncbi.nlm.nih.gov/nuccore/JN635406 Direct Submission Submitted (30-AUG-2011) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/
London.GBR/3.14/2/B3 measles KT732220 2014-01-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732220 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
London.GBR/3.14/3/B3 measles KT732221 2014-01-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732221 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
Roraima.BRA/31.18/D8 measles MK161348 2018-08-04 South America Brazil Brazil Brazil genbank genome Meneses et al https://www.ncbi.nlm.nih.gov/nuccore/MK161348 Complete genome of a Measles virus from Roraima state, Brazil bioRxivorg (2018) In press https://www.ncbi.nlm.nih.gov/pubmed/
Ancona.ITA/45.17/1/D8 measles MH173047 2017-11-XX Europe Italy Italy Italy genbank genome Marinelli et al https://www.ncbi.nlm.nih.gov/nuccore/MH173047 Direct Submission Submitted (06-APR-2018) Ao Ospedali Riuniti Di Ancona, Virologia, Via Conca, 71, Ancona 60020, Italy https://www.ncbi.nlm.nih.gov/pubmed/
Zhejiang.CHN/12.09/1/H1 measles KJ755980 2009-03-18 China China China China genbank genome Jin et al https://www.ncbi.nlm.nih.gov/nuccore/KJ755980 Evolutionary history of the endemic strains of Chinese Measles virus Unpublished https://www.ncbi.nlm.nih.gov/pubmed/
Shanghai-191 measles FJ416067 ? China China China China genbank genome Zhang et al https://www.ncbi.nlm.nih.gov/nuccore/FJ416067 Genetic characterization of Chinese measles vaccines by analysis of complete genomic sequences J. Med. Virol. 81 (8), 1477-1483 (2009) https://www.ncbi.nlm.nih.gov/pubmed/19551837
New_Jersey.USA/45.05 measles JN635408 2005-11-05 North America Usa Usa Usa genbank genome Kirkness et al https://www.ncbi.nlm.nih.gov/nuccore/JN635408 Direct Submission Submitted (30-AUG-2011) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/
Gambia/1993 measles EF565859 1993-XX-XX Africa Gambia Gambia Gambia genbank genome Druelle et al https://www.ncbi.nlm.nih.gov/nuccore/EF565859 Wild type measles virus attenuation independent of type I IFN Virol. J. 5, 22 (2008) https://www.ncbi.nlm.nih.gov/pubmed/18241351
London.GBR/3.14/B3 measles KT732219 2014-01-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732219 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
London.GBR/4.14/2/B3 measles KT732223 2014-01-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732223 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
T11 measles AB481088 1989-XX-XX Japan Korea Japan Japan Japan genbank genome Okada et al https://www.ncbi.nlm.nih.gov/nuccore/AB481088 Previously unrecognized amino acid substitutions in the hemagglutinin and fusion proteins of measles virus modulate cell-cell fusion, hemadsorption, virus growth, and penetration rate J. Virol. 83 (17), 8713-8721 (2009) https://www.ncbi.nlm.nih.gov/pubmed/19553316
Paris.FRA/18.11/D4 measles MF449469 2011-05-03 Europe France France France genbank genome Mura et al https://www.ncbi.nlm.nih.gov/nuccore/MF449469 Non-encapsidated 5' copy-back defective-interfering genomes produced by recombinant measles viruses are recognized by RIG-I and LGP2 but not MDA5 J. Virol. (2017) In press https://www.ncbi.nlm.nih.gov/pubmed/28768856
Teeside.GBR/16.13/6/D8 measles KT732253 2013-04-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732253 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
Zhejiang.CHN/12.08/1/H1 measles KJ755979 2008-03-20 China China China China genbank genome Jin et al https://www.ncbi.nlm.nih.gov/nuccore/KJ755979 Evolutionary history of the endemic strains of Chinese Measles virus Unpublished https://www.ncbi.nlm.nih.gov/pubmed/
London.GBR/20.11/2/D4 measles KT732226 2011-05-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732226 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
Derby.GBR/47.12/D8 measles KT732241 2012-11-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732241 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
Swansea.GBR/16.13/5/D8 measles KT732255 2013-04-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732255 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
9301V measles AB012949 ? ? ? ? ? genbank genome Takeda et al https://www.ncbi.nlm.nih.gov/nuccore/AB012949 Measles virus attenuation associated with transcriptional impediment and a few amino acid changes in the polymerase and accessory proteins J. Virol. 72 (11), 8690-8696 (1998) https://www.ncbi.nlm.nih.gov/pubmed/9765410
Swansea.GBR/16.13/2/D8 measles KT732251 2013-04-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732251 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
accession strain virus_name date region country division location length host date_released date_updated sra_accessions authors abbr_authors institution
MK161348.1 D8 2018-08-04 South America Brazil Boa Vista Roraima State 15894 Homo sapiens 2018-11-20 2019-04-10 Meneses,C.A.,Nascimento,V.A.,Souza,V.C.,Maito,R.M.,Gomes,M.A.,Cunha,C.R.,Antony,I.A.,Silva,M.E.,Campos,D.P.,Corado,A.L.,Pessoa,K.P.,Monteiro,D.C.,Okumoto,O.,Cunha,M.C.,Pacheco,F.C.,Naveca,F.G.,Corado,A.G. Meneses et al Instituto Leonidas e Maria Deane - Fiocruz Amazonia, Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia
MH173047.1 D8 2017-11-XX Europe Italy 15872 Homo sapiens 2018-06-06 2018-06-06 Marinelli,K.,Caucci,S.,Vincenzi,C.,Ferreri,M.,Magurano,F.,Bagnarelli,P.,Menzo,S. Marinelli et al Virologia, Ao Ospedali Riuniti Di Ancona
MF449469.1 G2V D4 2011-05-03 Europe France 15894 Homo sapiens 2017-08-28 2017-08-28 Mura,M.,Combredet,C.,Najburg,V.,Sanchez David,R.Y.,Tangy,F.,Komarova,A.V.,Sanchez-David,R.Y.,Komarova,A. Mura et al Institut Pasteur, Virology
KT732255.1 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732253.1 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732251.1 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732241.1 D8 2012-11-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732226.1 D4 2011-05-XX Europe United Kingdom 15684 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732223.1 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732221.1 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732220.1 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732219.1 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KJ755980.1 H1 2009-03-18 Asia China 15894 Homo sapiens 2016-05-02 2016-05-02 Jin,Q.,Xu,C.,Li,H.,Zhong,S.,Zheng,B.,Lu,Y. Jin et al Centre for Disease Control and Prevention of Zhejiang Province (ZJ CDC), Institute of Microbiology
KJ755979.1 H1 2008-03-20 Asia China 15894 Homo sapiens 2016-05-02 2016-05-02 Jin,Q.,Xu,C.,Li,H.,Zhong,S.,Zheng,B.,Lu,Y. Jin et al Centre for Disease Control and Prevention of Zhejiang Province (ZJ CDC), Institute of Microbiology
JN635408.1 2005-11-05 North America USA New Jersey 15894 Homo sapiens 2011-09-29 2012-01-26 Kirkness,E.F.,Halpin,R.,Bera,J.,Fedorova,N.,Overton,L.,Stockwell,T.,Amedeo,P.,Bishop,B.,Chen,H.,Edworthy,P.,Gupta,N.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Bankamp,B.,Byrd,L.,Bellini,W.,Rota,P. Kirkness et al J. Craig Venter Institute
JN635406.1 2008-03-11 North America USA Arizona 15894 Homo sapiens 2011-09-29 2012-01-26 Kirkness,E.F.,Halpin,R.,Bera,J.,Fedorova,N.,Overton,L.,Stockwell,T.,Amedeo,P.,Bishop,B.,Chen,H.,Edworthy,P.,Gupta,N.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Bankamp,B.,Byrd,L.,Bellini,W.,Rota,P. Kirkness et al J. Craig Venter Institute
FJ416067.1 15894 2009-05-21 2009-11-05 Zhang,Y.,Zhou,J.,Bellini,W.J.,Xu,W.,Rota,P.A.,Bamkamp,B. Zhang et al National Institute for Viral Disease Control and Prevention, China Centers for Disease Control and Prevention, WHO WPRO Regional Reference Measles Lab
EF565859.1 G954-PBL 1993-XX-XX Africa 6552 2008-04-02 2008-04-02 Druelle,J.,Sellin,C.I.,Waku-Kouomou,D.,Horvat,B.,Wild,F.T.,Sellin,C.,Wild,T. Druelle et al Inserm U404, Immunite et Vaccination
AB481088.1 1989-XX-XX Asia Japan 15894 2009-08-14 2009-08-14 Okada,H.,Itoh,M.,Nagata,K.,Takeuchi,K.,Ito,M. Okada et al Graduate School of Comprehensive Human Sciences; Tennodai 1-1-1, Tsukuba, Ibaraki 305-8575
AB012949.1 9301V 15894 Homo sapiens 1998-10-19 2008-12-04 Takeda,M.,Kato,A.,Kobune,F.,Sakata,H.,Li,Y.,Shioda,T.,Sakai,Y.,Asakawa,M.,Nagai,Y. Takeda et al University of Tokyo, Viral Infection; Shirokanedai 4-6-1, Minato-ku, Tokyo 108
Loading

0 comments on commit e2d56c7

Please sign in to comment.