From c61e67bb4be9173c328fb2834e210978decab151 Mon Sep 17 00:00:00 2001 From: theosanderson-agent Date: Fri, 8 May 2026 15:28:08 +0100 Subject: [PATCH 1/3] Add Andes virus example data --- README.md | 2 +- example_files/andes_virus_test_metadata.tsv | 2 + .../andes_virus_test_sequences.fasta | 156 ++++++++++++++++++ 3 files changed, 159 insertions(+), 1 deletion(-) create mode 100644 example_files/andes_virus_test_metadata.tsv create mode 100644 example_files/andes_virus_test_sequences.fasta diff --git a/README.md b/README.md index e0fd543..efaf85e 100644 --- a/README.md +++ b/README.md @@ -2,4 +2,4 @@ Example files for users to try out on the Pathoplexus [demo instance](https://demo.pathoplexus.org/). _(Please **do not** upload these to the main website!)_ -Currently example data is available for West Nile virus, Ebola Zaire, and CCHF. Metadata can be supplied in TSV or XLSX format - here we use XLSX for West Nile and TSV elsewhere, but all instances support both formats, and also a range of compression options. +Currently example data is available for West Nile virus, Ebola Zaire, CCHF, and Andes virus. Metadata can be supplied in TSV or XLSX format - here we use XLSX for West Nile and TSV elsewhere, but all instances support both formats, and also a range of compression options. diff --git a/example_files/andes_virus_test_metadata.tsv b/example_files/andes_virus_test_metadata.tsv new file mode 100644 index 0000000..ff8fe90 --- /dev/null +++ b/example_files/andes_virus_test_metadata.tsv @@ -0,0 +1,2 @@ +fastaIds ampliconPcrPrimerScheme ampliconSize anatomicalMaterial anatomicalPart authorAffiliations authors bodyProduct breadthOfCoverage cellLine collectionDevice collectionMethod consensusSequenceSoftwareName consensusSequenceSoftwareVersion cultureId dehostingMethod depthOfCoverage diagnostic_measurement_method diagnosticMeasurementUnit diagnosticMeasurementValue diagnosticTargetGeneName diagnosticTargetPresence environmentalMaterial environmentalSite experimentalSpecimenRoleType exposureDetails exposureEvent exposureSetting foodProduct foodProductProperties geoLocAdmin1 geoLocAdmin2 geoLocCity geoLocCountry geoLocSite hostAge hostAgeBin hostDisease hostGender hostHealthOutcome hostHealthState hostNameCommon hostNameScientific hostOriginCountry hostRole hostTaxonId hostVaccinationStatus passageMethod passageNumber presamplingActivity previousInfectionDisease previousInfectionOrganism purposeOfSampling purposeOfSequencing qualityControlDetails qualityControlDetermination qualityControlIssues qualityControlMethodName qualityControlMethodVersion rawSequenceDataProcessingMethod referenceGenomeAccession sampleCollectionDate sampleReceivedDate sampleType sequencedByContactEmail sequencedByContactName sequencedByOrganization sequencingAssayType sequencingDate sequencingInstrument sequencingProtocol signsAndSymptoms specimenCollectorSampleId specimenProcessing specimenProcessingDetails bioprojectAccessions id travelHistory versionComment +test_ANDV-Chile-9717869_L test_ANDV-Chile-9717869_M test_ANDV-Chile-9717869_S Centers for Disease Control and Prevention Nichol, S.T.; Spiropoulou, C.F.; Morzunov, S.; Rollin, P.E.; Ksiazek, T.G.; Feldmann, H.; Sanchez, A.; Childs, J.; Zaki, S.; Peters, C.J. Chile Homo sapiens 9606 NC_003468.2,NC_003467.2,NC_003466.1 1997 Chile-9717869 test_ANDV-Chile-9717869 Example data from Pathoplexus diff --git a/example_files/andes_virus_test_sequences.fasta b/example_files/andes_virus_test_sequences.fasta new file mode 100644 index 0000000..75e9d5b --- /dev/null +++ b/example_files/andes_virus_test_sequences.fasta @@ -0,0 +1,156 @@ +>test_ANDV-Chile-9717869_L +TAGTAGTAGACTCCGGGATAGAAAAAGTTAGAAAAATGGAAAAGTATAGAGAGATTCATCAGAGAGTTAGGGACCTTGCA +CCTGGAACGGTATCAGCATTAGAATGCATAGATCTACTGGATAGGCTCTACGCTGTCAGACATGACCTGGTTGACCAGAT +GATAAAACATGACTGGTCTGATAATAAAGATGTAGAAAGACCTATAGGTCAAGTTTTACTGATGGCTGGCATACCTAATG +ATATTATACAAGGCATGGAGAAGAAGATTATACCAAATAGCCCTTCTGGACAAGTATTGAAAAGCTTTTTCCGAATGACA +CCAGATAATTATAAAATTACAGGTAACTTGATTGAGTTTATTGAAGTGACTGTAACAGCTGATGTGTCACGAGGTATTAG +GGAGAAGAAAATAAAGTATGAAGGAGGCCTCCAATTTGTTGAGCACTTACTGGAAACTGAATCAAGGAAGGGTAATATAC +CGCAACCTTATAAAATAACATTCTCAGTGGTTGCAGTTAAAACAGATGGATCAAACATCTCGACTCAGTGGCCCAGTCGG +AGGAACGATGGGGTAGTTCAGCACATGCGTCTAGTCCAAGCTGATATAAATTATGTCAGAGAGCATTTAATAAAGTTAGA +TGAGAGAGCATCTTTGGAGGCAATGTTTAACTTAAAGTTCCATGTATCAGGCCCTAAACTGAGATACTTTAACATCCCTG +ATTATAGACCACAGCAGCTATGTGAACCACGGATTGACAACTTAATACAATATTGCAAGAATTGGTTGACAAAAGAACAT +AAGTTTGTATTCAAAGAAGTCAGTGGAGCTAATGTGATTCAAGCATTTGAGAGTCATGAACAGTTACATTTACAGAAATA +CAACGAATCACGAAAACCAAGAAATTTTTTACTCTTGCAGCTTACAGTGCAAGGGGCATATCTACCATCAACAATCAGTT +CTGACCAGTGCAATACTAGGATTGGGTGTCTAGAAATATCAAAAAACCAACCAGAAACACCAGTACAGATGCTTGCATTG +GATATATCTTATAAGTATCTGAGTCTTACAAGGGATGAGTTGATCAATTATTATAGCCCTAGAGTGCACTTTCAATCGAG +CCCTAATGTGAAGGAACCAGGGACACTGAAGTTAGGATTATCACAATTAAATCCACTCTCTAAATCAATTCTTGACAATG +TTGGAAAGCATAAAAAGGATAAAGGATTATTTGGTGAGATCATAGATAGCATAAATGTGGCAAGTCAAATACAGATCAAT +GCATGTGCAAAAATAATTGAGCAGATCTTATCAAATCTTGAAATAAACATTGGAGAAATAAATGCTAGTATGCCTTCTCC +TAATAAGACAACAGGTGTAGATGACCTGTTAAATAAATTTTATGATAATGAGCTTGGTAAATATATGTTATCCATTCTGA +GGAAAACAGCAGCATGGCATATAGGCCATCTAGTCAGAGATATCACAGAAAGTTTAATTGCACATGCTGGGCTGCGCCGT +TCTAAATATTGGTCAGTACATGCATATGACCATGGGAATGTAATTTTGTTTATCTTGCCATCAAAGTCACTAGAGGTAGT +AGGTTCTTATATAAGGTATTTCACAGTATTTAAAGATGGTATAGGGTTGATAGACGCAGATAATATTGATTCTAAGGCCG +AAATTGATGGTGTCACCTGGTGTTATTCTAAGGTCATGAGTATTGATTTAAACAGGTTATTGGCTTTGAACATAGCTTTT +GAGAAGTCACTTCTTGCCACGGCTACATGGTTCCAATATTATACTGAAGACCAAGGCCATTTTCCCCTTCAACATGCATT +AAGGTCAATCTTTTCTTTCCACTTTTTACTCTGTGTGTCACAAAAGATGAAGCTATGTGCAATATTTGATAACCTTCGTT +ATCTGATACCATCAGTAACATCTTTGTACTCTGGGTACGAGTTGTTAATAGAAAAATTCTTTGAGAGACCATTTAAGAGT +TCACTGGATGTATACCTTTATTCTATCATAAAATCTCTATTAATTAGTTTGGCACAAAATAATAAAGTTCGATTTTACTC +AAGAGTTCGTTTGTTAGGATTGACAGTTGATCACTCCACGGTCGGAGCAAGTGGTGTTTACCCCTCTTTAATGTCCCGTG +TTGTTTACAAACATTACAGAAGTTTAATCTCTGAAGCTACAACTTGTTTTTTCTTATTTGAAAAGGGTTTGCATGGGAAT +TTACCAGAAGAGGCTAAAATACATCTTGAAACCATTGAATGGGCTCGGAAGTTCCAGGAGAAAGAAAAACAATATGGTGA +TATTCTTCTAAAGGAAGGCTATACAATTGAATCTGTAATCAATGGAGAAGTTGATGTAGAACAACAGCTTTTTTGTCAGG +AGGTCTCAGAGCTAAGTGCACAAGAGCTCAACAAATATTTACAGGCAAAATCTCAAGTTTTATGTGCTAATATCATGAAT +AAACACTGGGACAAACCATATTTCAGTCAAACACGCAATATCAGTCTCAAGGGAATGTCTGGGGCATTGCAAGAGGATGG +ACATTTAGCTGCTAGTGTGACACTGATTGAAGCAATTAGGTTTTTAAATAGATCACAAACCAATCCAAATGTTATTGATA +TGTATGAGCAGACTAAACAATCAAAGGCACAAGCTAGGATTGTTAGGAAATACCAGAGAACAGAAGCAGATAGAGGATTT +TTTATCACAACATTACCAACTAGGGTGCGATTAGAAATAATAGAAGATTATTTCGATGCAATTGCAAAGGTTGTGCCTGA +AGAATATATTTCTTATGGTGGGGATAAAAAAGTTCTAAATATTCAGAATGCACTAGAGAAAGCACTTAGATGGGCATCTG +GAGTATCAGAAATTACAACAAGCACTGGTAAAAGCATCAAGTTTAAGCGGAAATTAATGTATGTTAGTGCTGATGCCACA +AAATGGTCACCAGGAGATAATTCTGCTAAGTTTAGGAGATTTACACAAGCAATATATGATGGCTTATCAGACAACAAACT +GAAATGTTGTGTTGTTGATGCATTACGTAACATTTATGAGACTGAATTTTTTATGTCCAGGAAATTACACCGATATATTG +ATAGTATGGAAAATCATTCAGATGCGGTTGAAGATTTCTTGGCATTTTTCTCAAATGGAGTCTCAGCCAATGTAAAGGGA +AACTGGCTTCAAGGGAACTTAAATAAATGCTCATCATTATTTGGTGCTGCTGTCTCATTACTTTTTCGGGAGGTCTGGAA +ACAATTGTTTCCAGAATTAGAGTGTTTTTTTGAATTTGCACATCATTCAGATGATGCATTGTTCATTTATGGCTATCTGG +AGCCTGAAGATGATGGAACAGATTGGTTTTTGTATGTATCACAGCAGATACAGGCAGGAAACTTTCATTGGCATGCTATA +AATCAAGAGATGTGGAAGAGCATGTTTAATCTACATGAGCACTTACTATTAATGGGTTCTATTAAAGTGTCACCTAAGAA +GACAACAGTATCACCTACTAATGCAGAATTTCTTTCTACTTTTTTTGAAGGTTGTGCTGTGTCAATCCCTTTTGTTAAAA +TCTTACTGGGTTCATTATCAGATCTTCCTGGGTTAGGTTTCTTTGATGATTTAGCAGCAGCACAAAGCAGATGTGTAAAG +TCACTAGATTTGGGTGCTTGCCCACAATTAGCTCAACTAGCTATAGTATTATGCACAAGCAAAGTTGAGAGGTTGTATGG +TACTGCTGATGGAATGGTAAACTCTCCAACAGCATTCCTTAAGGTGAATAAAGCACACGTACCAGTACCACTTGGTGGTG +ATGGCTCAATGTCTATTATGGAGCTTGCAACAGCTGGTTTTGGGATGGCAGATAAGAATATTTTAAAAAATGCATTCATA +TCTTATAAGCATACTCGTAGAGATGGTGATAGGTACGTATTGGGTTTATTTAAATTTTTGATGTCATTAAGTGAGGATGT +ATTCCAGCACGACCGATTGGGTGAGTTTAGTTTTGTAGGTAAAGTTCAATGGAAAGTGTTCACTCCTAAAGCTGAATTTG +AATTTCATGATCAATTTTCACATAATTATTTATTAGAGTGGACACGTCAACATCCTGTGTATGACTATATTATTCCTAGA +AATAGAGATAATTTGCTTGTATACCTTGTAAGAAAGTTGAATGATCCTAGCATCATTACAGCTATGACTATGCAGTCACC +ATTACAACTTCGTTTCCGTATGCAAGCAAAGCAACATATGAAAGTATGCCGGTATGAAGGTGAATGGGTCACATTCAGGG +AGGTACTTGCTGCAGCTGATAGTTTTGCTACGAGTTACCAACCTACTGAAAGGGACATGGATCTCTTTAATACACTTGTA +AGTTGTACATTTTCTAAAGAGTATGCTTGGAAAGACTTTTTAAATGAAGTAAGGTGTGAGGTCTTAACAACAAGACATGT +ACATAGGCCTAAAATTGCTAGGACATTCACTGTTAGAGAAAAGGACCAGGCTATACAAAATCCAATAAATTCGGTGATTG +GCTATAAGTATGCTCTTACAGTGGATGAAGTCAGTGATGTTCTTGATAGTGCATTCTTCCCAGAGTCTCTATCTGCAGAC +TTACAGGTTATGAAAGATGGAGTTTACAGAGAATTAGGACTTGATATAAGTTCTCCTGAAGTCCTAAAACGCATAGCACC +ACTATTATATAAGGCAGGAAGGTCACGTGTTGTTATTGTGGAAGGAAATGTAGAAGGGACAGCTGAGTCAATCTGTAGTT +ATTGGCTCAAGACAATGTCACTGATTAAAACAATCAGAGTAAGACCTAAGAAGGAGGTACTGAAAGCTATGTCTTTATAT +AGTGTTAAAGAAAATATTGGATTGCAGGATGATATTGCAGCAACTCGACTATGCATAGAAATCTGGAGATGGTGTAAGGC +AAATGAACAGGATGTTAAAGAATGGCTAACATCTCTGTACTTTGAAAAACAGACATTGATGGATTGGGTAGAAAGGTTTA +GAAGGAAAGGAGTTGTTCCTATTGATCCTGAAATACAATGTATTGGCCTACTCTTATATGATGTATTAGGTTATAAAAGT +GTGTTACAAATGCAAGCAAACCGAAGAGCCTATTCAGGTAAGCAATATGATGCATACTGTGTGCAAACATATAACGAGGA +AACAAAACTATATGAAGGTGACCTTCGTGTTACTTTTAATTTTGGTTTAGATTGTGCAAGGTTAGAAGTTTTTTGGGATA +AAAAAGAGTATATCTTAGAGACATCTATCACCCAACGACATGTGTTGCGGTTACTGATGGAAGAAGTGTCACAAGAATTA +ATTAGATGTGGAATGAGATTCAAAACAGAGCAAGTCAATCAAACTCGGAGCTTAGTGTTATTCAAAACAGAGGCTGGTTT +TGAATGGGGTAAGCCTAATGTGCCATGTATTGTATATAAACACTGTGTCTTGAGAACTGGGCTTCGTACGAAACAGCCAA +TTAATAAAGAGTTCATGATAAATGTACAAAGTGATGGTTTCCGTGCAATAGCACAGATGGATATTGAGAGTCCACGGTTC +TTGTTAGCACATGCATATCATACACTGCGTGATATTAGATATCAAGCAGTGCAGGCAGTAGGGAATGTATGGTTTAAAAC +AGAACAGCACAAACTATTTATTAACCCAATTATATCATCAGGGCTTTTAGAAAACTTTATGAAAGGCTTACCTGCTGCCA +TACCTCCTGCTGCATATTCCCTCATAATGAACAAGGCTAAGATTTCTGTGGATTTGTTTATGTTCAATGAGCTATTAGCA +CTTATAAATAGGAATAATATCCTCAACCTTGATGGGATTGAAGAAACATCTGAAGGTTATAGTACTGTGACATCAATGTC +TAGCAAGCAGTGGTCTGAAGAGATGAGTTTAATGTCTGATGATGATATTGATGATATGGAGGACTTTACTATAGCACTGG +ATGATATTGACTTTGAACAAATAAATTTGGAAGAGGATATACAACACTTTCTGCAGGATGAATCAGCATATGTTGGTGAT +TTATTGATTCAGACAGAAGACATTGAGGTTAAAAAGATACGTGGGGTGACAAGAGTATTAGAGCCAGTCAAGCTATTAAA +AAGCTGGGTTTCTAAAGGCCTTGCTATAGACAAAGTATACAATCCTATCGGGATAATCTTAATGGCAAGATACATGTCAA +AAACATACAATTTCAGTTCAACACCTCTTGCACTATTAAATCCATATGACTTGACAGAACTTGAAAGTGTTGTAAAGGGA +TGGGGAGAAACTGTAAATGATCGATTCAAAGATTTAGATATTGAGGCACAAACAGTTGTTAAAGAAAAGGGTGTACAGCC +AGAAGATGTACTCCCTGATTCATTATTCTCTTTCAGGCATGTTGATGTTTTGCTGCGAAGGTTGTTCCCGCGTGACCCTG +TATCAACATTCTATTAGTGGATTTTATACCTTATTCATACAGTATGTATATTGTAGTGTTCTTTTCCCGGAGCATACTAC +TA +>test_ANDV-Chile-9717869_M +TAGTAGTAGACTCCGCAAGAAGAAGCAAAAAATTAAAGAAGTGAGTTTAAAATGGAAGGGTGGTATCTGGTTGTTCTTGG +AGTCTGCTATACGCTGACACTGGCAATGCCCAAGACCATTTATGAGCTTAAAATGGAATGCCCGCACACTGTGGGTCTCG +GTCAAGGTTACATCATTGGCTCAACAGAACTAGGTTTGATCTCAATTGAGGCTGCATCTGATATAAAGCTCGAGAGCTCT +TGCAATTTTGATCTTCATACAACATCTATGGCCCAGAAGAGTTTCACCCAAGTTGAATGGAGAAAGAAAAGTGACACAAC +TGATACCACAAATGCTGCGTCCACTACCTTTGAAGCACAAACTAAAACTGTTAACCTTAGAGGGACTTGTATACTGGCAC +CTGAACTCTATGATACATTGAAGAAAGTAAAAAAGACAGTCCTGTGCTATGATCTAACATGTAATCAAACACATTGTCAG +CCAACTGTCTATCTGATTGCACCTGTATTGACATGCATGTCAATAAGAAGTTGTATGGCTAGTGTGTTTACAAGCAGGAT +TCAGGTGATTTATGAAAAGACACATTGTGTAACAGGTCAGCTGATTGAGGGTCAGTGTTTCAACCCAGCACACACATTGA +CATTATCTCAGCCTGCTCACACTTATGATACTGTCACCCTTCCTATCTCTTGTTTTTTCACACCAAAGAAGTCGGAGCAA +CTAAAAGTTATAAAAACATTTGAAGGAATTCTGACGAAGACAGGTTGCACGGAGAATGCATTGCAGGGTTATTATGTGTG +TTTTTTAGGGAGTCATTCAGAACCTTTAATTGTTCCGAGTTTGGAGGACATACGGTCTGCTGAAGTTGTTAGTAGGATGC +TTGTACACCCTAGGGGAGAAGACCATGATGCCATACAGAATTCACAAAGTCACTTAAGAATAGTGGGACCTATCACAGCA +AAAGTGCCATCAACTAGTTCCACAGATACCCTAAAGGGGACAGCCTTTGCAGGCGTCCCAATGTATAGCTCTTTATCTAC +ACTAGTCAGAAATGCAGACCCAGAATTTGTATTTTCTCCAGGTATAGTACCTGAATCTAATCACAGTACATGTGATAAGA +AGACAGTACCTATCACATGGACAGGCTACCTACCAATATCAGGTGAGATGGAAAAAGTGACTGGATGTACAGTTTTTTGT +ACACTAGCAGGACCTGGTGCTAGTTGTGAGGCCTATTCTGAAAATGGTATATTTAACATCAGTTCTCCAACATGTCTTGT +AAACAAAGTCCAAAGATTTCGTGGATCTGAACAGAAAATAAATTTTATCTGTCAGCGGGTAGATCAGGATGTTGTTGTAT +ACTGCAATGGGCAAAAGAAAGTCATATTAACCAAAACTTTGGTTATTGGGCAGTGTATTTATACATTCACAAGCCTATTT +TCATTGATGCCTGATGTAGCCCACTCATTGGCTGTAGAATTATGTGTCCCGGGATTACATGGATGGGCCACTGTCATGCT +TCTATCAACATTCTGCTTTGGGTGGGTCTTGATTCCTGCGGTCACATTAATAATATTAAAGTGTCTAAGGGTTTTGACGT +TTTCTTGTTCCCATTACACTAATGAGTCAAAATTTAAATTCATCCTGGAAAAAGTTAAAATTGAATACCAAAAGACTATG +GGATCAATGGTGTGCGATGTATGTCATCATGAGTGTGAAACAGCAAAAGAACTTGAATCACATAGACAGAGTTGTATCAA +TGGACAATGTCCTTATTGCATGACAATAACTGAAGCAACTGAAAGTGCCTTGCAAGCCCATTATTCCATTTGTAAATTGA +CAGGAAGATTTCAGGAGGCACTGAAAAAGTCACTTAAAAAGCCAGAGGTAAAAAAAGGTTGTTACAGAACACTCGGGGTA +TTTAGATATAAAAGTAGATGTTATGTGGGTTTGGTATGGTGCCTATTGTTGACATGTGAAATTGTTATTTGGGCCGCAAG +TGCAGAGACTCCACTAATGGAGTCAGGCTGGTCAGATACGGCTCATGGTGTTGGTGAGATTCCAATGAAGACAGACCTCG +AGCTGGACTTTTCACTGCCTTCTTCATCCTCTTACAGTTATAGGAGAAAGCTCACAAACCCAGCCAATAAAGAAGAGTCT +ATTCCCTTCCACTTCCAGATGGAAAAACAAGTAATTCATGCTGAAATCCAACCCCTGGGTCATTGGATGGATGCGACATT +TAATATTAAGACTGCATTTCATTGTTATGGTGCATGCCAGAAATACTCTTATCCATGGCAGACATCTAAGTGCTTCTTTG +AAAAGGACTACCAGTATGAAACAGGCTGGGGCTGTAATCCTGGTGACTGCCCAGGGGTTGGGACTGGATGCACTGCTTGT +GGTGTTTATCTCGATAAACTAAAATCTGTTGGGAAGGCCTATAAGATAATTTCTTTAAAATATACCAGAAAGGTTTGTAT +TCAGTTAGGAACAGAACAAACTTGCAAGCATATTGATGCAAATGATTGTTTAGTGACACCATCTGTGAAAGTTTGCATAG +TGGGCACAGTTTCAAAACTTCAACCATCTGATACTCTTTTGTTCTTAGGTCCACTAGAACAAGGGGGAATCATTCTTAAG +CAATGGTGCACAACATCATGTGCATTTGGGGACCCTGGTGATATCATGTCCACTCCCAGTGGTATGAGGTGTCCAGAGCA +CACTGGATCATTTAGGAAAATTTGCGGTTTTGCTACTACACCAGTTTGTGAATATCAAGGAAATACCATTTCTGGATATA +AAAGAATGATGGCAACAAAAGATTCATTCCAATCATTTAACTTAACAGAACCTCACATCACAACAAACAAGCTTGAATGG +ATCGACCCAGATGGGAATACAAGAGACCACGTAAACCTTGTCTTAAATAGAGATGTCTCATTTCAGGATTTAAGTGATAA +CCCCTGTAAAGTAGACCTACACACACAAGCAATAGAAGGGGCATGGGGTTCTGGTGTAGGGTTTACACTCACATGTACTG +TCGGATTAACAGAGTGCCCAAGTTTTATGACATCAATTAAGGCATGTGACCTAGCTATGTGTTATGGATCAACAGTAACA +AACCTTGCCAGGGGCTCTAATACAGTGAAAGTAGTTGGTAAAGGAGGCCATTCAGGGTCCTCATTTAAATGCTGTCATGA +TACAGATTGCTCCTCTGAAGGTTTACTTGCATCAGCCCCTCATCTTGAGAGGGTAACAGGATTCAATCAAATTGATTCAG +ATAAGGTTTATGATGATGGTGCACCACCTTGCACATTCAAATGCTGGTTCACTAAGTCAGGTGAGTGGCTTCTTGGGATC +TTAAACGGGAATTGGATTGTTGTTGTAGTGCTTGTTGTGATACTCATTCTCTCTATCATAATGTTCAGTGTTTTGTGTCC +CAGGAGAGGGCACAAGAAAACTGTCTAAGCATTGACCTCAACTCCTACATTAGATCATATACATTTATGCACTTCCTCAT +ATTTAGCTGCACTAAGATATTAATAAACTCTAGTTATTGACTTTATAAGATTATTATGGAACTAACCTCACTTAAAAAAA +ACAAATACTTTACTCATATATAACTCCATATTCTCTTACCGAGGCTTTTGTTCCTGCGGAGCATACTACTA +>test_ANDV-Chile-9717869_S +TAGTAGTAGACTCCTTGAGAAGCTACTGCTGCGAAAGCTGGAATGAGCACCCTCCAAGAATTGCAGGAAAACATCACAGC +ACACGAACAACAGCTCGTGACTGCTCGGCAAAAGCTTAAGGATGCCGAGAAGGCAGTGGAGGTGGACCCGGATGACGTTA +ACAAGAGCACACTACAAAGTAGACGGGCAGCTGTGTCTACATTGGAGACCAAACTCGGAGAACTTAAGAGGCAACTTGCA +GATTTGGTGGCAGCTCAAAAATTGGCTACAAAACCAGTTGATCCAACAGGGCTTGAGCCTGATGATCATCTAAAGGAAAA +ATCATCTCTGAGATATGGGAATGTCCTGGATGTTAATTCAATTGATTTGGAAGAACCGAGTGGACAGACTGCTGATTGGA +AGGCTATAGGAGCATACATCTTAGGGTTTGCAATTCCGATCATCCTAAAGGCCTTATACATGCTGTCAACCCGTGGGAGA +CAAACTGTGAAAGACAACAAAGGGACCAGGATAAGGTTTAAGGATGATTCTTCCTTTGAAGAAGTCAATGGGATACGTAA +ACCAAAACACCTTTACGTCTCAATGCCAACTGCACAGTCCACTATGAAGGCTGAAGAAATCACGCCAGGACGATTTAGGA +CAATTGCTTGTGGCCTTTTTCCAGCACAGGTCAAAGCCCGAAATATAATAAGTCCTGTAATGGGAGTAATTGGATTTGGC +TTCTTTGTAAAGGATTGGATGGATCGGATAGAAGAGTTTCTGGCTGCAGAGTGTCCATTCTTACCTAAGCCAAAGGTCGC +CTCAGAAGCCTTCATGTCTACCAATAAGATGTATTTTCTGAACAGACAGAGACAAGTCAATGAATCTAAGGTTCAAGATA +TTATCGATTTGATAGACCATGCTGAGACCGAGTCTGCTACCTTGTTTACAGAGATTGCAACACCCCATTCAGTCTGGGTG +TTTGCATGTGCACCTGACCGGTGCCCTCCAACTGCATTGTATGTTGCAGGGGTACCGGAACTTGGTGCATTTTTTTCTAT +CCTTCAGGACATGCGTAATACCATCATGGCATCTAAATCTGTAGGGACTGCAGAAGAGAAGCTAAAGAAAAAATCTGCCT +TCTACCAATCATACCTAAGAAGGACACAATCTATGGGAATCCAACTGGACCAGAAGATCATAATCCTTTACATGCTATCA +TGGGGTAAAGAAGCTGTGAATCACTTCCATCTTGGTGATGATATGGACCCTGAACTCAGGCAGCTAGCACAATCTCTGAT +CGATACTAAGGTGAAGGAGATCTCCAACCAAGAGCCACTTAAGTTGTAGGTGCTTAATGAAATCATGATTGAAGAAAGAC +TTTCCGGGCTTGTGCCACATATTAATCATCTCAGGACCTATCCTTAATGTGATTAATAGGGTTTTATTATAAGGGCAGTT +AATGGGGTTGGTTACTAACTATGGGTAAGGGTTCATTACCATTTTTGCACTAGGGTTAAAGGGCCACTACATTGTATTTG +CACTAAGGGAAATGGGAGGTGGGTTAGTTTGTATTTAGTTGTTAAGTTTTTTATAATCATATGTTAATGAGGAATTAGCT +ATATGATATCACTGATTGATTGGCTATTTTTAGGTTAAGTAATTGTAGTTAAATAGTTGTGTTAAGTTAGTATGTTAAGG +TTTATAGGTTAAGATTTACTAACAATCATATTATGTCATTAGATGTAAATTTCATTCCTGGCTTGCTTCTGCTTTCGCAT +TGCTAACCTACAACAAGACTACCTCACCCACTACCCCTCCCCTATTCTACCTCAACACATACTACCTCACATTTGATTTT +TCTTGATTGCTTTTCAAGGAGCATACTACTA From b9b346c72c4ae6471ef9f41f1b6973158e9023c1 Mon Sep 17 00:00:00 2001 From: theosanderson-agent Date: Fri, 8 May 2026 15:40:18 +0100 Subject: [PATCH 2/3] Use synthetic Andes example metadata --- example_files/andes_virus_test_metadata.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/example_files/andes_virus_test_metadata.tsv b/example_files/andes_virus_test_metadata.tsv index ff8fe90..9607228 100644 --- a/example_files/andes_virus_test_metadata.tsv +++ b/example_files/andes_virus_test_metadata.tsv @@ -1,2 +1,2 @@ fastaIds ampliconPcrPrimerScheme ampliconSize anatomicalMaterial anatomicalPart authorAffiliations authors bodyProduct breadthOfCoverage cellLine collectionDevice collectionMethod consensusSequenceSoftwareName consensusSequenceSoftwareVersion cultureId dehostingMethod depthOfCoverage diagnostic_measurement_method diagnosticMeasurementUnit diagnosticMeasurementValue diagnosticTargetGeneName diagnosticTargetPresence environmentalMaterial environmentalSite experimentalSpecimenRoleType exposureDetails exposureEvent exposureSetting foodProduct foodProductProperties geoLocAdmin1 geoLocAdmin2 geoLocCity geoLocCountry geoLocSite hostAge hostAgeBin hostDisease hostGender hostHealthOutcome hostHealthState hostNameCommon hostNameScientific hostOriginCountry hostRole hostTaxonId hostVaccinationStatus passageMethod passageNumber presamplingActivity previousInfectionDisease previousInfectionOrganism purposeOfSampling purposeOfSequencing qualityControlDetails qualityControlDetermination qualityControlIssues qualityControlMethodName qualityControlMethodVersion rawSequenceDataProcessingMethod referenceGenomeAccession sampleCollectionDate sampleReceivedDate sampleType sequencedByContactEmail sequencedByContactName sequencedByOrganization sequencingAssayType sequencingDate sequencingInstrument sequencingProtocol signsAndSymptoms specimenCollectorSampleId specimenProcessing specimenProcessingDetails bioprojectAccessions id travelHistory versionComment -test_ANDV-Chile-9717869_L test_ANDV-Chile-9717869_M test_ANDV-Chile-9717869_S Centers for Disease Control and Prevention Nichol, S.T.; Spiropoulou, C.F.; Morzunov, S.; Rollin, P.E.; Ksiazek, T.G.; Feldmann, H.; Sanchez, A.; Childs, J.; Zaki, S.; Peters, C.J. Chile Homo sapiens 9606 NC_003468.2,NC_003467.2,NC_003466.1 1997 Chile-9717869 test_ANDV-Chile-9717869 Example data from Pathoplexus +test_ANDV-Chile-9717869_L test_ANDV-Chile-9717869_M test_ANDV-Chile-9717869_S Imaginary Institute of Example Virology Bloggs, Joe; Example, Jane; Placeholder, Alex Fantasyland Chile Homo sapiens 9606 NC_003468.2,NC_003467.2,NC_003466.1 1997 Chile-9717869 test_ANDV-Chile-9717869 Example data from Pathoplexus From 021d0c703a2bc1a21c676b7bdcccf76c64582f34 Mon Sep 17 00:00:00 2001 From: theosanderson-agent Date: Fri, 8 May 2026 15:40:47 +0100 Subject: [PATCH 3/3] Add substitutions to Andes example sequences --- example_files/andes_virus_test_sequences.fasta | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/example_files/andes_virus_test_sequences.fasta b/example_files/andes_virus_test_sequences.fasta index 75e9d5b..ae1f78c 100644 --- a/example_files/andes_virus_test_sequences.fasta +++ b/example_files/andes_virus_test_sequences.fasta @@ -1,11 +1,11 @@ >test_ANDV-Chile-9717869_L TAGTAGTAGACTCCGGGATAGAAAAAGTTAGAAAAATGGAAAAGTATAGAGAGATTCATCAGAGAGTTAGGGACCTTGCA -CCTGGAACGGTATCAGCATTAGAATGCATAGATCTACTGGATAGGCTCTACGCTGTCAGACATGACCTGGTTGACCAGAT +CCTGGAACGGTATCAGCATTCGAATGCATAGATCTACTGGATAGGCTCTACGCTGTCAGACATGACCTGGTTGACCAGAT GATAAAACATGACTGGTCTGATAATAAAGATGTAGAAAGACCTATAGGTCAAGTTTTACTGATGGCTGGCATACCTAATG ATATTATACAAGGCATGGAGAAGAAGATTATACCAAATAGCCCTTCTGGACAAGTATTGAAAAGCTTTTTCCGAATGACA CCAGATAATTATAAAATTACAGGTAACTTGATTGAGTTTATTGAAGTGACTGTAACAGCTGATGTGTCACGAGGTATTAG GGAGAAGAAAATAAAGTATGAAGGAGGCCTCCAATTTGTTGAGCACTTACTGGAAACTGAATCAAGGAAGGGTAATATAC -CGCAACCTTATAAAATAACATTCTCAGTGGTTGCAGTTAAAACAGATGGATCAAACATCTCGACTCAGTGGCCCAGTCGG +CGCAACCTTATAAAATAACAATCTCAGTGGTTGCAGTTAAAACAGATGGATCAAACATCTCGACTCAGTGGCCCAGTCGG AGGAACGATGGGGTAGTTCAGCACATGCGTCTAGTCCAAGCTGATATAAATTATGTCAGAGAGCATTTAATAAAGTTAGA TGAGAGAGCATCTTTGGAGGCAATGTTTAACTTAAAGTTCCATGTATCAGGCCCTAAACTGAGATACTTTAACATCCCTG ATTATAGACCACAGCAGCTATGTGAACCACGGATTGACAACTTAATACAATATTGCAAGAATTGGTTGACAAAAGAACAT @@ -14,7 +14,7 @@ CAACGAATCACGAAAACCAAGAAATTTTTTACTCTTGCAGCTTACAGTGCAAGGGGCATATCTACCATCAACAATCAGTT CTGACCAGTGCAATACTAGGATTGGGTGTCTAGAAATATCAAAAAACCAACCAGAAACACCAGTACAGATGCTTGCATTG GATATATCTTATAAGTATCTGAGTCTTACAAGGGATGAGTTGATCAATTATTATAGCCCTAGAGTGCACTTTCAATCGAG CCCTAATGTGAAGGAACCAGGGACACTGAAGTTAGGATTATCACAATTAAATCCACTCTCTAAATCAATTCTTGACAATG -TTGGAAAGCATAAAAAGGATAAAGGATTATTTGGTGAGATCATAGATAGCATAAATGTGGCAAGTCAAATACAGATCAAT +ATGGAAAGCATAAAAAGGATAAAGGATTATTTGGTGAGATCATAGATAGCATAAATGTGGCAAGTCAAATACAGATCAAT GCATGTGCAAAAATAATTGAGCAGATCTTATCAAATCTTGAAATAAACATTGGAGAAATAAATGCTAGTATGCCTTCTCC TAATAAGACAACAGGTGTAGATGACCTGTTAAATAAATTTTATGATAATGAGCTTGGTAAATATATGTTATCCATTCTGA GGAAAACAGCAGCATGGCATATAGGCCATCTAGTCAGAGATATCACAGAAAGTTTAATTGCACATGCTGGGCTGCGCCGT @@ -84,12 +84,12 @@ TATCAACATTCTATTAGTGGATTTTATACCTTATTCATACAGTATGTATATTGTAGTGTTCTTTTCCCGGAGCATACTAC TA >test_ANDV-Chile-9717869_M TAGTAGTAGACTCCGCAAGAAGAAGCAAAAAATTAAAGAAGTGAGTTTAAAATGGAAGGGTGGTATCTGGTTGTTCTTGG -AGTCTGCTATACGCTGACACTGGCAATGCCCAAGACCATTTATGAGCTTAAAATGGAATGCCCGCACACTGTGGGTCTCG +AGTCTGCTATACGCTGACACAGGCAATGCCCAAGACCATTTATGAGCTTAAAATGGAATGCCCGCACACTGTGGGTCTCG GTCAAGGTTACATCATTGGCTCAACAGAACTAGGTTTGATCTCAATTGAGGCTGCATCTGATATAAAGCTCGAGAGCTCT TGCAATTTTGATCTTCATACAACATCTATGGCCCAGAAGAGTTTCACCCAAGTTGAATGGAGAAAGAAAAGTGACACAAC TGATACCACAAATGCTGCGTCCACTACCTTTGAAGCACAAACTAAAACTGTTAACCTTAGAGGGACTTGTATACTGGCAC CTGAACTCTATGATACATTGAAGAAAGTAAAAAAGACAGTCCTGTGCTATGATCTAACATGTAATCAAACACATTGTCAG -CCAACTGTCTATCTGATTGCACCTGTATTGACATGCATGTCAATAAGAAGTTGTATGGCTAGTGTGTTTACAAGCAGGAT +CCAACTGTCTATCTGATTGCCCCTGTATTGACATGCATGTCAATAAGAAGTTGTATGGCTAGTGTGTTTACAAGCAGGAT TCAGGTGATTTATGAAAAGACACATTGTGTAACAGGTCAGCTGATTGAGGGTCAGTGTTTCAACCCAGCACACACATTGA CATTATCTCAGCCTGCTCACACTTATGATACTGTCACCCTTCCTATCTCTTGTTTTTTCACACCAAAGAAGTCGGAGCAA CTAAAAGTTATAAAAACATTTGAAGGAATTCTGACGAAGACAGGTTGCACGGAGAATGCATTGCAGGGTTATTATGTGTG @@ -98,7 +98,7 @@ TTGTACACCCTAGGGGAGAAGACCATGATGCCATACAGAATTCACAAAGTCACTTAAGAATAGTGGGACCTATCACAGCA AAAGTGCCATCAACTAGTTCCACAGATACCCTAAAGGGGACAGCCTTTGCAGGCGTCCCAATGTATAGCTCTTTATCTAC ACTAGTCAGAAATGCAGACCCAGAATTTGTATTTTCTCCAGGTATAGTACCTGAATCTAATCACAGTACATGTGATAAGA AGACAGTACCTATCACATGGACAGGCTACCTACCAATATCAGGTGAGATGGAAAAAGTGACTGGATGTACAGTTTTTTGT -ACACTAGCAGGACCTGGTGCTAGTTGTGAGGCCTATTCTGAAAATGGTATATTTAACATCAGTTCTCCAACATGTCTTGT +CCACTAGCAGGACCTGGTGCTAGTTGTGAGGCCTATTCTGAAAATGGTATATTTAACATCAGTTCTCCAACATGTCTTGT AAACAAAGTCCAAAGATTTCGTGGATCTGAACAGAAAATAAATTTTATCTGTCAGCGGGTAGATCAGGATGTTGTTGTAT ACTGCAATGGGCAAAAGAAAGTCATATTAACCAAAACTTTGGTTATTGGGCAGTGTATTTATACATTCACAAGCCTATTT TCATTGATGCCTGATGTAGCCCACTCATTGGCTGTAGAATTATGTGTCCCGGGATTACATGGATGGGCCACTGTCATGCT @@ -131,12 +131,12 @@ ATTTAGCTGCACTAAGATATTAATAAACTCTAGTTATTGACTTTATAAGATTATTATGGAACTAACCTCACTTAAAAAAA ACAAATACTTTACTCATATATAACTCCATATTCTCTTACCGAGGCTTTTGTTCCTGCGGAGCATACTACTA >test_ANDV-Chile-9717869_S TAGTAGTAGACTCCTTGAGAAGCTACTGCTGCGAAAGCTGGAATGAGCACCCTCCAAGAATTGCAGGAAAACATCACAGC -ACACGAACAACAGCTCGTGACTGCTCGGCAAAAGCTTAAGGATGCCGAGAAGGCAGTGGAGGTGGACCCGGATGACGTTA +ACACGAACAACAGCTCGTGAGTGCTCGGCAAAAGCTTAAGGATGCCGAGAAGGCAGTGGAGGTGGACCCGGATGACGTTA ACAAGAGCACACTACAAAGTAGACGGGCAGCTGTGTCTACATTGGAGACCAAACTCGGAGAACTTAAGAGGCAACTTGCA GATTTGGTGGCAGCTCAAAAATTGGCTACAAAACCAGTTGATCCAACAGGGCTTGAGCCTGATGATCATCTAAAGGAAAA ATCATCTCTGAGATATGGGAATGTCCTGGATGTTAATTCAATTGATTTGGAAGAACCGAGTGGACAGACTGCTGATTGGA AGGCTATAGGAGCATACATCTTAGGGTTTGCAATTCCGATCATCCTAAAGGCCTTATACATGCTGTCAACCCGTGGGAGA -CAAACTGTGAAAGACAACAAAGGGACCAGGATAAGGTTTAAGGATGATTCTTCCTTTGAAGAAGTCAATGGGATACGTAA +CAAACTGTGAAAGACAACAACGGGACCAGGATAAGGTTTAAGGATGATTCTTCCTTTGAAGAAGTCAATGGGATACGTAA ACCAAAACACCTTTACGTCTCAATGCCAACTGCACAGTCCACTATGAAGGCTGAAGAAATCACGCCAGGACGATTTAGGA CAATTGCTTGTGGCCTTTTTCCAGCACAGGTCAAAGCCCGAAATATAATAAGTCCTGTAATGGGAGTAATTGGATTTGGC TTCTTTGTAAAGGATTGGATGGATCGGATAGAAGAGTTTCTGGCTGCAGAGTGTCCATTCTTACCTAAGCCAAAGGTCGC @@ -145,7 +145,7 @@ TTATCGATTTGATAGACCATGCTGAGACCGAGTCTGCTACCTTGTTTACAGAGATTGCAACACCCCATTCAGTCTGGGTG TTTGCATGTGCACCTGACCGGTGCCCTCCAACTGCATTGTATGTTGCAGGGGTACCGGAACTTGGTGCATTTTTTTCTAT CCTTCAGGACATGCGTAATACCATCATGGCATCTAAATCTGTAGGGACTGCAGAAGAGAAGCTAAAGAAAAAATCTGCCT TCTACCAATCATACCTAAGAAGGACACAATCTATGGGAATCCAACTGGACCAGAAGATCATAATCCTTTACATGCTATCA -TGGGGTAAAGAAGCTGTGAATCACTTCCATCTTGGTGATGATATGGACCCTGAACTCAGGCAGCTAGCACAATCTCTGAT +AGGGGTAAAGAAGCTGTGAATCACTTCCATCTTGGTGATGATATGGACCCTGAACTCAGGCAGCTAGCACAATCTCTGAT CGATACTAAGGTGAAGGAGATCTCCAACCAAGAGCCACTTAAGTTGTAGGTGCTTAATGAAATCATGATTGAAGAAAGAC TTTCCGGGCTTGTGCCACATATTAATCATCTCAGGACCTATCCTTAATGTGATTAATAGGGTTTTATTATAAGGGCAGTT AATGGGGTTGGTTACTAACTATGGGTAAGGGTTCATTACCATTTTTGCACTAGGGTTAAAGGGCCACTACATTGTATTTG