diff --git a/example_files/west_nile_metadata.tsv b/example_files/west_nile_metadata.tsv index 16b205c..059b81d 100644 --- a/example_files/west_nile_metadata.tsv +++ b/example_files/west_nile_metadata.tsv @@ -1,12 +1,12 @@ -submissionId versionComment authors authorAffiliations specimenCollectorSampleId Geo_Location geoLocCountry geoLocAdmin1 geoLocAdmin2 geoLocCity hostNameScientific anatomicalMaterial sampleCollectionDate -test_INYO_2_2011 KR348976 "Duggal, N.K.; Reisen, W.K.; Fang, Y.; Newman,R.M.; Yang, X.; Ebel, G.D.; Brault,A.C.; Brault,A." "Centers for Disease Control and Prevention, Division of Vector-Borne Infectious Diseases" INYO_2_2011 USA Hogwarts Culex tarsalis 2011-07-18 -test_WNV/mosquito/Bakersfield_CA_USA/2010-07-08/W417 MH508004 "Grubaugh,N.; Fang,Y.; Matteson,N.L.; Gangavarapu,K.; Coffey,L.; Barker,C.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: Bakersfield,California" USA California Hogwarts Bakersfield Culex quinquefasciatus pooled insects 2010-07-08 -test_WNV/mosquito/Larimer-CO-USA/2016-06-27/W1819 OQ721426 "Grubaugh,N.; Matteson,N.; Gangavarupa,K.; Ebel,G.; Murrieta,R.; Fauver,J.; Young,M.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: Larimer, Colorado" USA Colorado Hogwarts Larimer Culex tarsalis pooled insects 2016-06-27 -test_AVA1305539 MF175822 "Aroh,C.; D'Anton,M.; Liang,C.; Raj,P.; Wakeland,B.; Yan,N.; Wakeland,E." "UT Southwestern Medical Center, Department of Immunology" AVA1305539 USA: Dallas Co. TX USA texas Hogwarts Dallas Co Culex quinquefasciatus 2013-08-20 -test_WNV/mosquito/Polk-IA-USA/2017-07-17/W1959 OQ721462 "Grubaugh,N.; Matteson,N.; Gangavarupa,K.; Smith,R.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: Polk, Iowa" USA Iowa Hogwarts Polk Culex restuans pooled insects 2017-07-17 -test_WNV/mosquito/San_Diego_CA_USA/2014-10-31/W014 MH507621 "Grubaugh,N.; Grewal,S.; Matteson,N.L.; Gangavarapu,K.; Gurfield,N.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: San_Diego,California" USA California Hogwarts San Diego Culex quinquefasciatus pooled insects 2014-10-31 -test_WNV/bird/Valley_Center_CA_USA/2008-09-18/W037 MH507637 "Grubaugh,N.; Grewal,S.; Matteson,N.L.; Gangavarapu,K.; Gurfield,N.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: Valley_Center,California" USA California Hogwarts Valey Center Corvus brachyrhynchos tissue 2008-09-18 -test_WNV-1/Cyanocitta cristata /USA/03003243/2003 KX547593 "Shabman,R.; Das,S.R.; Halpin,R.A.; Shilts,M.; Fedorova,N.; Puri,V.; Amedeo,P.; Shrivastava,S.; Maffei,J.; Dupuis,A.; Jones,S.; Backenson,B.; Zink,S.; Ciota,A.; Kramer,L." J. Craig Venter Institute "USA: Washington Co., NY" USA New York Hogwarts Washington Co Cyanocitta cristata 2003-09-28 -test_WNV/mosquito/Parlier_CA_USA/2010-08-12/W188 MH507768 "Grubaugh,N.; Fang,Y.; Matteson,N.L.; Gangavarapu,K.; Coffey,L.; Barker,C.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: Parlier,California" USA California Hogwarts Parlier Culex tarsalis pooled insects 2010-08-12 -test_WNV/mosquito/Yolo-CA-USA/2015-07-16/W0706 OQ721464 "Grubaugh,N.; Matteson,N.; Gangavarupa,K.; Barker,C.; Wheeler,S.; Fang,Y.; Coffey,L.; Reisen,W.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: Yolo, California" USA California Hogwarts Yolo Culex tarsalis pooled insects 2015-07-16 -test_AZ10-91 KF704147 "Plante,J.A.; Burkhalter,K.L.; Mann,B.R.; Godsey,M.S. Jr.; Mutebi,J.P.; Beasley,D.W.; Mutebi,J.-P." Centers for Disease Control and Prevention "USA: Glendale, Maricopa Co., AZ" USA Arizona Hogwarts Glendale Culex quinquefasciatus 2010-08-01 +submissionId versionComment authors authorAffiliations specimenCollectorSampleId Geo_Location geoLocCountry geoLocAdmin1 geoLocAdmin2 geoLocCity hostNameScientific anatomicalMaterial sampleCollectionDate sequencingInstrument files.rawReads +test_INYO_2_2011 KR348976 "Duggal, N.K.; Reisen, W.K.; Fang, Y.; Newman,R.M.; Yang, X.; Ebel, G.D.; Brault,A.C.; Brault,A." "Centers for Disease Control and Prevention, Division of Vector-Borne Infectious Diseases" INYO_2_2011 USA Hogwarts Culex tarsalis 2011-07-18 ILLUMINA raw_reads_1.fq.gz +test_WNV/mosquito/Bakersfield_CA_USA/2010-07-08/W417 MH508004 "Grubaugh,N.; Fang,Y.; Matteson,N.L.; Gangavarapu,K.; Coffey,L.; Barker,C.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: Bakersfield,California" USA California Hogwarts Bakersfield Culex quinquefasciatus pooled insects 2010-07-08 PacBio RS raw_reads_contaminated.fq.gz +test_WNV/mosquito/Larimer-CO-USA/2016-06-27/W1819 OQ721426 "Grubaugh,N.; Matteson,N.; Gangavarupa,K.; Ebel,G.; Murrieta,R.; Fauver,J.; Young,M.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: Larimer, Colorado" USA Colorado Hogwarts Larimer Culex tarsalis pooled insects 2016-06-27 +test_AVA1305539 MF175822 "Aroh,C.; D'Anton,M.; Liang,C.; Raj,P.; Wakeland,B.; Yan,N.; Wakeland,E." "UT Southwestern Medical Center, Department of Immunology" AVA1305539 USA: Dallas Co. TX USA texas Hogwarts Dallas Co Culex quinquefasciatus 2013-08-20 +test_WNV/mosquito/Polk-IA-USA/2017-07-17/W1959 OQ721462 "Grubaugh,N.; Matteson,N.; Gangavarupa,K.; Smith,R.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: Polk, Iowa" USA Iowa Hogwarts Polk Culex restuans pooled insects 2017-07-17 +test_WNV/mosquito/San_Diego_CA_USA/2014-10-31/W014 MH507621 "Grubaugh,N.; Grewal,S.; Matteson,N.L.; Gangavarapu,K.; Gurfield,N.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: San_Diego,California" USA California Hogwarts San Diego Culex quinquefasciatus pooled insects 2014-10-31 +test_WNV/bird/Valley_Center_CA_USA/2008-09-18/W037 MH507637 "Grubaugh,N.; Grewal,S.; Matteson,N.L.; Gangavarapu,K.; Gurfield,N.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: Valley_Center,California" USA California Hogwarts Valey Center Corvus brachyrhynchos tissue 2008-09-18 +test_WNV-1/Cyanocitta_cristata/USA/03003243/2003 KX547593 "Shabman,R.; Das,S.R.; Halpin,R.A.; Shilts,M.; Fedorova,N.; Puri,V.; Amedeo,P.; Shrivastava,S.; Maffei,J.; Dupuis,A.; Jones,S.; Backenson,B.; Zink,S.; Ciota,A.; Kramer,L." J. Craig Venter Institute "USA: Washington Co., NY" USA New York Hogwarts Washington Co Cyanocitta cristata 2003-09-28 +test_WNV/mosquito/Parlier_CA_USA/2010-08-12/W188 MH507768 "Grubaugh,N.; Fang,Y.; Matteson,N.L.; Gangavarapu,K.; Coffey,L.; Barker,C.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: Parlier,California" USA California Hogwarts Parlier Culex tarsalis pooled insects 2010-08-12 +test_WNV/mosquito/Yolo-CA-USA/2015-07-16/W0706 OQ721464 "Grubaugh,N.; Matteson,N.; Gangavarupa,K.; Barker,C.; Wheeler,S.; Fang,Y.; Coffey,L.; Reisen,W.; Andersen,K." "The Scripps Research Institute, Department of Immunology and Microbiology" "USA: Yolo, California" USA California Hogwarts Yolo Culex tarsalis pooled insects 2015-07-16 +test_AZ10-91 KF704147 "Plante,J.A.; Burkhalter,K.L.; Mann,B.R.; Godsey,M.S. Jr.; Mutebi,J.P.; Beasley,D.W.; Mutebi,J.-P." Centers for Disease Control and Prevention "USA: Glendale, Maricopa Co., AZ" USA Arizona Hogwarts Glendale Culex quinquefasciatus 2010-08-01 \ No newline at end of file diff --git a/example_files/west_nile_metadata.xls b/example_files/west_nile_metadata.xls index fca9b2e..6e53a03 100644 Binary files a/example_files/west_nile_metadata.xls and b/example_files/west_nile_metadata.xls differ diff --git a/example_files/west_nile_metadata.xlsx b/example_files/west_nile_metadata.xlsx index ff67254..6cc4257 100644 Binary files a/example_files/west_nile_metadata.xlsx and b/example_files/west_nile_metadata.xlsx differ diff --git a/example_files/west_nile_raw_reads/raw_reads_1.fq.gz b/example_files/west_nile_raw_reads/raw_reads_1.fq.gz new file mode 100644 index 0000000..c4bac0f Binary files /dev/null and b/example_files/west_nile_raw_reads/raw_reads_1.fq.gz differ diff --git a/example_files/west_nile_raw_reads/raw_reads_contaminated.fq.gz b/example_files/west_nile_raw_reads/raw_reads_contaminated.fq.gz new file mode 100644 index 0000000..7cc1e8c Binary files /dev/null and b/example_files/west_nile_raw_reads/raw_reads_contaminated.fq.gz differ diff --git a/example_files/west_nile_sequences.fasta b/example_files/west_nile_sequences.fasta index 565dacb..e803b16 100644 --- a/example_files/west_nile_sequences.fasta +++ b/example_files/west_nile_sequences.fasta @@ -1389,7 +1389,7 @@ TCTGGTGTGGCAGCCTGATCGGCACAAGAGCCCGAGCCACGTGGGCAGAAAACATCCAGG TGGCTATCAACCAAGTCAGAGCAATCATTGGAGATGAGAAGTATGTGGATTACATGAGTT CACTAAAGAGATATGAAGACACAACTTTGGTTGAGGATACAGTACTGTAG ->test_WNV-1/Cyanocitta cristata /USA/03003243/2003 +>test_WNV-1/Cyanocitta_cristata/USA/03003243/2003 AGTGTTTGTGAGGATTAACAACGATTAACACAGTGCGAGCTGTTTCTTAGCACGAAGATC TCGATGTCTAAGAAACCAGGAGGGCCCGGCAAGAGCCGGGCTGTCAATATGCTAAAACGC GGAATGCCCCGCGTGTTGTCCTTGATTGGACTGAAGAGGGCTATGTTGAGCCTGATCGAC