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To use the new metadata format where we group by strain. Steps to regenerate: 1. Populate 'data/' with metadata & sequences from an ingest run. 2. Subsample this as example data via: ``` augur filter --metadata data/metadata.tsv --group-by country --subsample-max-sequences 30 --output-metadata example_data/metadata.tsv augur filter --metadata example_data/metadata.tsv --sequences data/L/sequences.fasta --output-sequences example_data/sequences_L.fasta augur filter --metadata example_data/metadata.tsv --sequences data/M/sequences.fasta --output-sequences example_data/sequences_M.fasta augur filter --metadata example_data/metadata.tsv --sequences data/S/sequences.fasta --output-sequences example_data/sequences_S.fasta ```
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| rule copy_example_data: | ||
| rule copy_example_sequences: | ||
| input: | ||
| sequences="example_data/sequences_{segment}.fasta", | ||
| metadata="example_data/metadata_{segment}.tsv", | ||
| output: | ||
| sequences="data/{segment}/sequences.fasta", | ||
| metadata="data/{segment}/metadata.tsv", | ||
| shell: | ||
| """ | ||
| cp -f {input.sequences} {output.sequences} | ||
| """ | ||
|
|
||
| rule copy_example_metadata: | ||
| input: | ||
| metadata="example_data/metadata.tsv", | ||
| output: | ||
| metadata="data/metadata.tsv", | ||
| shell: | ||
| """ | ||
| cp -f {input.metadata} {output.metadata} | ||
| """ | ||
|
|
||
| # Add a Snakemake ruleorder directive here if you need to resolve ambiguous rules | ||
| # that have the same output as the copy_example_data rule. | ||
|
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| ruleorder: copy_example_data > decompress | ||
| ruleorder: copy_example_sequences > download_sequences_for_segment | ||
| ruleorder: copy_example_metadata > download_metadata |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,31 @@ | ||
| strain n_segments date region country division location host authors abbr_authors institution accession_L accession_version_L length_L date_released_L date_updated_L sra_accessions_L segment_L qc_L accession_M accession_version_M length_M date_released_M date_updated_M sra_accessions_M segment_M qc_M accession_S accession_version_S length_S date_released_S date_updated_S sra_accessions_S segment_S qc_S | ||
| TRVL9760 3 1955-XX-XX South America Trinidad and Tobago Trinidad Sangre Grande Acrani,G.O.,Tilston-Lunel,N.L.,Spiegel,M.,Weidmann,M.,Dilcher,M.,Andrade da Silva,D.E.,Nunes,M.R.,Elliott,R.M.,Olszanski Acrani,G.,Nunes,M.R.T. Acrani et al. University Medical Center Goettingen, Department of Virology KP026179 KP026179.1 6852 2015-03-10 2015-03-10 1 good KP026180 KP026180.1 4385 2015-03-10 2015-03-10 1 good KP026181 KP026181.1 958 2015-03-10 2015-03-10 1 good | ||
| BeH505442 1 XXXX-XX-XX Saeed,M.F.,Wang,H.,Nunes,M.,Vasconcelos,P.F.,Weaver,S.C.,Shope,R.E.,Watts,D.M.,Tesh,R.B.,Barrett,A.D.,Barrett,A.D.T. Saeed et al. University of Texas Medical Branch, Microbiology & Immunology AF164542 AF164542.1 693 2000-03-26 2000-03-26 1 good | ||
| IQT7085 1 XXXX-XX-XX Saeed,M.F.,Wang,H.,Nunes,M.,Vasconcelos,P.F.,Weaver,S.C.,Shope,R.E.,Watts,D.M.,Tesh,R.B.,Barrett,A.D.,Barrett,A.D.T. Saeed et al. University of Texas Medical Branch, Microbiology & Immunology AF164554 AF164554.1 693 2000-03-26 2000-03-26 1 good | ||
| H532500 3 1994-XX-XX Homo sapiens Vasconcelos,H.B.,Nunes,M.R.,Casseb,L.M.,Carvalho,V.L.,Pinto da Silva,E.V.,Silva,M.,Casseb,S.M.,Vasconcelos,P.F.,Vasconcelos,P.F.C. Vasconcelos et al. Evandro Chagas Institute, Arbovirology and Hemorrhagic Fevers HQ830429 HQ830429.1 720 2011-05-10 2016-07-25 1 good HQ830394 HQ830394.1 526 2011-05-10 2016-07-25 1 good HQ830464 HQ830464.1 696 2011-06-08 2011-06-08 1 good | ||
| H543091 1 1996-XX-XX Homo sapiens Vasconcelos,H.B.,Nunes,M.R.,Casseb,L.M.,Carvalho,V.L.,Pinto da Silva,E.V.,Silva,M.,Casseb,S.M.,Vasconcelos,P.F.,Vasconcelos,P.F.C. Vasconcelos et al. Evandro Chagas Institute, Arbovirology and Hemorrhagic Fevers HQ830465 HQ830465.1 696 2011-06-08 2011-06-08 1 good | ||
| TRVL-9760 3 XXXX-XX-XX South America Trinidad and Tobago Trinidad Homo sapiens Dugan,V.G.,Halpin,R.A.,Ghedin,E.,Fedorova,N.,Overton,L.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Gorchakov,R.,Forrester,N.,Weaver,S.,Wentworth,D.E.,Tesh,R. Dugan et al. J. Craig Venter Institute KC759122 KC759122.1 6811 2013-03-17 2013-03-17 1 good KC759123 KC759123.1 4357 2013-03-17 2013-03-17 1 good KC759124 KC759124.1 749 2013-03-17 2013-03-17 1 good | ||
| GML-444479 3 XXXX-XX-XX North America Panama Homo sapiens Dugan,V.G.,Halpin,R.A.,Ghedin,E.,Fedorova,N.,Overton,L.,Tsitrin,T.,Stockwell,T.,Amedeo,P.,Appalla,L.,Bishop,B.,Edworthy,P.,Gupta,N.,Hoover,J.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Gorchakov,R.,Forrester,N.,Weaver,S.,Wentworth,D.E.,Tesh,R. Dugan et al. J. Craig Venter Institute KC759128 KC759128.1 6569 2013-03-17 2013-03-17 1 good KC759129 KC759129.1 4259 2013-03-17 2013-03-17 1 good KC759130 KC759130.1 749 2013-03-17 2013-03-17 1 good | ||
| TVP-19249/GML-444672 3 1989-XX-XX North America Panama Homo sapiens Travassos da Rosa,J.F.S.,Silva,S.P.,Lima,C.P.S.,Oliveira,L.F.,Vasconcelos,J.M.,Da Silva,D.E.A.,Travassos da Rosa,A.P.A.,Guzman,H.,Tesh,R.B.,Vasconcelos,P.F.C.,Cardoso,J.F.,Vianez-Junior,J.L.S.G.,Nunes,M.R.T. Travassos da Rosa et al. Evandro Chagas Institute, Center for Technological Innovation KP795075 KP795075.1 6835 2016-09-01 2020-05-12 1 good KP795076 KP795076.1 4387 2016-09-01 2020-05-12 1 good KP795077 KP795077.1 754 2016-09-01 2020-05-12 1 good | ||
| TVP-19250/GML-444839 3 1989-08-XX North America Panama Homo sapiens Travassos da Rosa,J.F.S.,Silva,S.P.,Lima,C.P.S.,Oliveira,L.F.,Vasconcelos,J.M.,Da Silva,D.E.A.,Travassos da Rosa,A.P.A.,Guzman,H.,Tesh,R.B.,Vasconcelos,P.F.C.,Cardoso,J.F.,Vianez-Junior,J.L.S.G.,Nunes,M.R.T. Travassos da Rosa et al. Evandro Chagas Institute, Center for Technological Innovation KP795078 KP795078.1 6836 2016-09-01 2020-05-12 1 good KP795079 KP795079.1 4380 2016-09-01 2020-05-12 1 good KP795080 KP795080.1 780 2016-09-01 2020-05-12 1 good | ||
| TVP-19257/IQT-1690 3 1995-06-XX South America Peru Homo sapiens Travassos da Rosa,J.F.S.,Silva,S.P.,Lima,C.P.S.,Oliveira,L.F.,Vasconcelos,J.M.,Da Silva,D.E.A.,Travassos da Rosa,A.P.A.,Guzman,H.,Tesh,R.B.,Vasconcelos,P.F.C.,Cardoso,J.F.,Vianez-Junior,J.L.S.G.,Nunes,M.R.T. Travassos da Rosa et al. Evandro Chagas Institute, Center for Technological Innovation KP795087 KP795087.1 6839 2016-09-01 2020-05-12 1 good KP795088 KP795088.1 4371 2016-09-01 2020-05-12 1 good KP795089 KP795089.1 934 2016-09-01 2020-05-12 1 good | ||
| TVP-19258/IQT-4083 3 1997-08-XX South America Peru Homo sapiens Travassos da Rosa,J.F.S.,Silva,S.P.,Lima,C.P.S.,Oliveira,L.F.,Vasconcelos,J.M.,Da Silva,D.E.A.,Travassos da Rosa,A.P.A.,Guzman,H.,Tesh,R.B.,Vasconcelos,P.F.C.,Cardoso,J.F.,Vianez-Junior,J.L.S.G.,Nunes,M.R.T. Travassos da Rosa et al. Evandro Chagas Institute, Center for Technological Innovation KP795090 KP795090.1 6903 2016-09-01 2020-05-12 1 good KP795091 KP795091.1 4382 2016-09-01 2020-05-12 1 good KP795092 KP795092.1 945 2016-09-01 2020-05-12 1 good | ||
| TVP-19260/MD-203 3 1994-02-XX South America Peru Homo sapiens Travassos da Rosa,J.F.S.,Silva,S.P.,Lima,C.P.S.,Oliveira,L.F.,Vasconcelos,J.M.,Da Silva,D.E.A.,Travassos da Rosa,A.P.A.,Guzman,H.,Tesh,R.B.,Vasconcelos,P.F.C.,Cardoso,J.F.,Vianez-Junior,J.L.S.G.,Nunes,M.R.T. Travassos da Rosa et al. Evandro Chagas Institute, Center for Technological Innovation KP795096 KP795096.1 6815 2016-09-01 2020-05-12 1 good KP795097 KP795097.1 4373 2016-09-01 2020-05-12 1 good KP795098 KP795098.1 928 2016-09-01 2020-05-12 1 good | ||
| TVP-19264/PAN-481126 3 1999-10-XX North America Panama Homo sapiens Travassos da Rosa,J.F.S.,Silva,S.P.,Lima,C.P.S.,Oliveira,L.F.,Vasconcelos,J.M.,Da Silva,D.E.A.,Travassos da Rosa,A.P.A.,Guzman,H.,Tesh,R.B.,Vasconcelos,P.F.C.,Cardoso,J.F.,Vianez-Junior,J.L.S.G.,Nunes,M.R.T. Travassos da Rosa et al. Evandro Chagas Institute, Center for Technological Innovation KP795102 KP795102.1 6843 2016-09-01 2020-05-12 1 good KP795103 KP795103.1 4359 2016-09-01 2020-05-12 1 good KP795104 KP795104.1 960 2016-09-01 2020-05-12 1 good | ||
| OROV/EC/Esmeraldas/087/2016 3 2016-04-01 South America Ecuador Homo sapiens Wise,E.L.,Pullan,S.T.,Marquez,S.,Paz,V.,Mosquera,J.D.,Mena,S.,Jackson,S.K.,Fejer,G.,Trueba,G.,Logue,C.H. Wise et al. Public Health England, NIS, Research MF926354 MF926354.1 6852 2017-10-16 2017-10-16 1 good MF926353 MF926353.1 4387 2017-10-16 2017-10-16 1 good MF926352 MF926352.1 952 2017-10-16 2017-10-16 1 good | ||
| OROV/EC/Esmeraldas/155/2016 3 2016-04-XX South America Ecuador Homo sapiens Wise,E.L.,Logue,C.H.,Mellors,J.,Atkinson,B.,Marquez,S.,Zapata,S.,Paz,V.,Trueba,G.,Gutierrez,B.,Pybus,O.G.,Jackson,S.K.,Fejer,G.,Pullan,S.T. Wise et al. Public Health England, NIS, Research MK506829 MK506829.1 6852 2019-11-08 2019-11-08 1 good MK506824 MK506824.1 4387 2019-11-08 2019-11-08 1 good MK506819 MK506819.1 952 2019-11-08 2019-11-08 1 good | ||
| OROV/EC/Esmeraldas/171/2016 3 2016-04-XX South America Ecuador Homo sapiens Wise,E.L.,Logue,C.H.,Mellors,J.,Atkinson,B.,Marquez,S.,Zapata,S.,Paz,V.,Trueba,G.,Gutierrez,B.,Pybus,O.G.,Jackson,S.K.,Fejer,G.,Pullan,S.T. Wise et al. Public Health England, NIS, Research MK506830 MK506830.1 6852 2019-11-08 2019-11-08 1 good MK506825 MK506825.1 4387 2019-11-08 2019-11-08 1 good MK506820 MK506820.1 952 2019-11-08 2019-11-08 1 good | ||
| OROV/EC/Esmeraldas/210/2016 3 2016-04-XX South America Ecuador Homo sapiens Wise,E.L.,Logue,C.H.,Mellors,J.,Atkinson,B.,Marquez,S.,Zapata,S.,Paz,V.,Trueba,G.,Gutierrez,B.,Pybus,O.G.,Jackson,S.K.,Fejer,G.,Pullan,S.T. Wise et al. Public Health England, NIS, Research MK506832 MK506832.1 6852 2019-11-08 2019-11-08 1 good MK506827 MK506827.1 4387 2019-11-08 2019-11-08 1 good MK506822 MK506822.1 952 2019-11-08 2019-11-08 1 good | ||
| OV/Homo_sapiens/Haiti-1/2014 3 2014-05-26 North America Haiti Homo sapiens White,S.K.,Elbadry,M.A.,Morris,J.G. Jr.,Lednicky,J.A. White et al. University of Florida - Gainesville, Environmental and Global Health MN264267 MN264267.1 6852 2020-03-22 2020-03-22 1 good MN264268 MN264268.1 4385 2020-03-22 2020-03-22 1 good MN264269 MN264269.1 958 2020-03-22 2020-03-22 1 good | ||
| LET-2083 3 2024-02-05 South America Colombia Homo sapiens Limonta,D.,Peres-Restrepo,L.S.,Ciouderis,K.,Hernandez-Ortiz,J.P.,Osorio,J.R.,Perez,L.J.,Perez-Restrepo,L.S.,Ciuoderis,K.,Usuga,J.,Moreno,I.,Vargas,V.,Arevalo-Arbelaez,A.J.,Berg,M.G.,Cloherty,G.A.,Osorio,J.E. Limonta et al. Universidad Nacional de Colombia, Laboratorio Genomico One Health PP477303 PP477303.1 6852 2024-09-24 2024-09-24 1 good PP477315 PP477315.1 4387 2024-09-24 2024-09-24 1 good PP477309 PP477309.1 953 2024-09-24 2024-09-24 1 good | ||
| LET-2102 3 2024-02-13 South America Colombia Homo sapiens Limonta,D.,Peres-Restrepo,L.S.,Ciouderis,K.,Hernandez-Ortiz,J.P.,Osorio,J.R.,Perez,L.J.,Perez-Restrepo,L.S.,Ciuoderis,K.,Usuga,J.,Moreno,I.,Vargas,V.,Arevalo-Arbelaez,A.J.,Berg,M.G.,Cloherty,G.A.,Osorio,J.E. Limonta et al. Universidad Nacional de Colombia, Laboratorio Genomico One Health PP477304 PP477304.1 6852 2024-09-24 2024-09-24 1 good PP477316 PP477316.1 4387 2024-09-24 2024-09-24 1 good PP477310 PP477310.1 953 2024-09-24 2024-09-24 1 good | ||
| LET-2088 3 2024-02-06 South America Colombia Homo sapiens Limonta,D.,Peres-Restrepo,L.S.,Ciouderis,K.,Hernandez-Ortiz,J.P.,Osorio,J.R.,Perez,L.J.,Perez-Restrepo,L.S.,Ciuoderis,K.,Usuga,J.,Moreno,I.,Vargas,V.,Arevalo-Arbelaez,A.J.,Berg,M.G.,Cloherty,G.A.,Osorio,J.E. Limonta et al. Universidad Nacional de Colombia, Laboratorio Genomico One Health PP477306 PP477306.1 6852 2024-09-24 2024-09-24 1 good PP477318 PP477318.1 4387 2024-09-24 2024-09-24 1 good PP477312 PP477312.1 952 2024-09-24 2024-09-24 1 good | ||
| LET-2093 3 2024-02-08 South America Colombia Homo sapiens Limonta,D.,Peres-Restrepo,L.S.,Ciouderis,K.,Hernandez-Ortiz,J.P.,Osorio,J.R.,Perez,L.J.,Perez-Restrepo,L.S.,Ciuoderis,K.,Usuga,J.,Moreno,I.,Vargas,V.,Arevalo-Arbelaez,A.J.,Berg,M.G.,Cloherty,G.A.,Osorio,J.E. Limonta et al. Universidad Nacional de Colombia, Laboratorio Genomico One Health PP477308 PP477308.1 6852 2024-09-24 2024-09-24 1 good PP477320 PP477320.1 4387 2024-09-24 2024-09-24 1 good PP477314 PP477314.1 952 2024-09-24 2024-09-24 1 good | ||
| IRCCS-SCDC_1297/2024 1 2024-05-29 North America Cuba Homo sapiens Mori,A.,Matucci,A.,Chesini,L.,Pomari,E.,Castilletti,C.,Gobbi,F.G. Mori et al. IRCCS Sacro Cuore Don Calabria Hospital, Department of Infectious-Tropical Diseases and Microbiology PP874910 PP874910.1 201 2024-06-23 2024-06-23 1 good | ||
| IRCCS-SCDC_1/2024 2 2024-06-11 North America Cuba Irccs Sacro Cuore Don Calabria Negrar di Valpolicella, Vr Homo sapiens Deiana,M.,Malago',S.,Piubelli,C.,Castilletti,C. Deiana et al. IRCCS Sacro Cuore Don Calabria Hospital, Department of Infectious - Tropical Diseases and Microbiology PP952118 PP952118.2 4373 2024-07-02 2024-07-19 1 good PP952117 PP952117.2 952 2024-07-02 2024-07-19 1 good | ||
| FPI21207 3 2023-12-28 South America Peru Loreto Maynas Homo sapiens Espinoza,A.,Castillo,R.,Cruz,C.D.,Troncos,G.,Espejo,V.,Silva,M.,Ampuero,J.S. Espinoza et al. NAMRU-SOUTH, VEID PP966980 PP966980.1 6519 2024-07-11 2024-07-11 1 good PP966972 PP966972.1 4215 2024-07-11 2024-07-11 1 good PP966964 PP966964.1 702 2024-07-11 2024-07-11 1 good | ||
| LACENAM_ILMD_0572MNA 3 2024-02-01 South America Brazil Am Manaquiri Homo sapiens Silva,D.,Nascimento,F.,Mejia,M.,Nascimento,V.,Souza,V.,Oliveira,Y.,Naveca,F. Silva et al. Instituto Leonidas e Maria Deane - Fiocruz Amazonia, Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia PQ065135 PQ065135.1 6702 2024-07-31 2024-07-31 1 good PQ065136 PQ065136.1 4317 2024-07-31 2024-07-31 1 good PQ065137 PQ065137.1 823 2024-07-31 2024-07-31 1 good | ||
| LACENAM_ILMD_3091LGS 3 2023-12-15 South America Brazil Am Manaus Homo sapiens Silva,D.,Nascimento,F.,Mejia,M.,Nascimento,V.,Souza,V.,Oliveira,Y.,Naveca,F. Silva et al. Instituto Leonidas e Maria Deane - Fiocruz Amazonia, Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia PQ065258 PQ065258.1 6702 2024-07-31 2024-07-31 1 good PQ065259 PQ065259.1 4317 2024-07-31 2024-07-31 1 good PQ065260 PQ065260.1 825 2024-07-31 2024-07-31 1 good | ||
| LACENAM_ILMD_3219MTM 3 2023-12-22 South America Brazil Am Manaus Homo sapiens Silva,D.,Nascimento,F.,Mejia,M.,Nascimento,V.,Souza,V.,Oliveira,Y.,Naveca,F. Silva et al. Instituto Leonidas e Maria Deane - Fiocruz Amazonia, Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia PQ065306 PQ065306.1 6702 2024-07-31 2024-07-31 1 good PQ065307 PQ065307.1 4317 2024-07-31 2024-07-31 1 good PQ065308 PQ065308.1 822 2024-07-31 2024-07-31 1 good | ||
| IRCCS-SCDC_1442/2024 1 2024-06-14 Europe Italy Homo sapiens Mori,A.,Matucci,A.,Chesini,L.,Pomari,E.,Van Duffel,L.,Cristini,F.,Castilletti,C.,Gobbi,F.G. Mori et al. IRCCS Sacro Cuore Don Calabria Hospital, Department of Infectious-Tropical Diseases and Microbiology PQ118421 PQ118421.1 184 2024-08-06 2024-08-06 1 good | ||
| LACENRJ_LARBOH_5338-2024 3 2024-04-02 South America Brazil Rio de Janeiro_Pirai Homo sapiens de Bruycker-Nogueira,F.,Bispo de Filippis,A.M.,Nascimento,V.,Souza,V.,Naveca,F.G. de Bruycker-Nogueira et al. Instituto Leonidas e Maria Deane - Fiocruz Amazonia, Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia PQ295367 PQ295367.1 6702 2024-09-30 2024-09-30 1 good PQ295368 PQ295368.1 4065 2024-09-30 2024-09-30 1 good PQ295369 PQ295369.1 824 2024-09-30 2024-09-30 1 good |
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