Skip to content

Commit 0aae1f9

Browse files
misemingermiseminger
committed
Add example data for influenza_1.2.3
1 parent 1b3c546 commit 0aae1f9

2 files changed

Lines changed: 14 additions & 0 deletions

File tree

‎web/templates/influenza/exampleInput/influenza-invalidTestData_1-2-3.tsv‎

Lines changed: 7 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,7 @@
1+
Database Identifiers Sample collection and processing Host Information Host vaccination information Host exposure information Sequencing Bioinformatics and QC metrics Pathogen diagnostic testing Contributor acknowledgement
2+
specimen collector sample ID third party lab service provider name third party lab sample ID case ID Related specimen primary ID IRIDA sample name umbrella bioproject accession bioproject accession biosample accession SRA accession GenBank accession GISAID accession GISAID virus name sample collected by sample collector contact email sequenced by sequence submitted by sample collection date sample collection date precision geo_loc_name (country) geo_loc_name (state/province/territory) organism isolate ID purpose of sampling purpose of sampling details NML submitted specimen type Related specimen relationship type presampling_activity presampling activity details anatomical material anatomical part body product collection device collection method collection protocol specimen processing specimen processing details biomaterial extracted host (common name) host (scientific name) host health state host health status details host health outcome host disease host age host age unit host age bin host gender host subject ID host vaccination status vaccination history exposure event exposure contact level host role exposure setting exposure details purpose of sequencing purpose of sequencing details sequencing date amplicon size library preparation kit sequencing instrument sequencing protocol amplicon pcr primer scheme raw sequence data processing method dehosting method consensus sequence software name consensus sequence software version breadth of coverage value depth of coverage value depth of coverage threshold number of base pairs sequenced consensus genome length reference genome accession bioinformatics protocol gene name 1 diagnostic pcr Ct value 1 gene name 2 diagnostic pcr Ct value 2 gene name 3 diagnostic pcr Ct value 3 authors DataHarmonizer provenance
3+
prov_fluA_11 Switch Health SHK123456 ABCD1234 SR20-12345 prov_flu_99 PRJNA623807 PRJNA608651 SAMN14180202 SRR11177792 NC_007362.1 EPI_ISL_436489 A/Ontario/Canada/ABCD1231/2023 Eastern Ontario Regional Laboratory Association RespLab@lab.ca Public Health Ontario (PHO) Public Health Ontario (PHO) 2020-03-16 day Canada Ontario Influenza A virus (H1N1) Not Provided Diagnostic testing Not Provided Swab Reinfection testing Vaccination Patient was previously infected. Sample taken during convalescence. Saliva;Not Applicable Nasopharynx (NP) Not Applicable Swab Swabbing FluSamplingProtocol v. 1.2 Virus passage Not Provided RNA (total) Human Homo sapiens Symptomatic Hospitalized (ICU) Recovered Influenza 79 year 70 - 79 Male BCxy123 Fully Vaccinated Social Gathering Direct contact (direct human-to-human contact) Inpatient Healthcare Setting Case infected family at home Baseline surveillance (random sampling) Seasonal flu research project 22-09-2023 300bp Nextera XT Oxford Nanopore MinION Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Porechop 0.2.3 Nanostripper iVar 1.3 95% 400x 100x https://github.com/BCCDC-PHL/nf-flu Haemagglutinin (HA) gene 21 Matrix (M) gene 36 Not Applicable Not Applicable Tejinder Singh, Fei Hu, Joe Blogs DataHarmonizer v1.9.7, Influenza v1.2.3
4+
prov_fluA_12 A/Ontario/Canada/ABCD1232/2023 Eastern Ontario Regional Laboratory Association RespLab@lab.ca Public Health Ontario (PHO) Public Health Ontario (PHO) 2020-03-18 day Canada Ontario Flu A (H1N1) Not Provided Diagnostic testing Not Provided Swab Saliva;Not Applicable Nasopharynx (NP) Not Applicable Swab Swabbing Homo sapiens Influenza 54 year 50 - 59 Female Baseline surveillance (random sampling) Seasonal flu research project 2023-09-22 Oxford Nanopore MinION Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Porechop 0.2.3 Nanostripper iVar 1.3 95% 400x 100x https://github.com/BCCDC-PHL/nf-flu Tejinder Singh, Fei Hu, Joe Blogs DataHarmonizer v1.9.7, Influenza v1.2.3
5+
prov_fluA_13 A/Ontario/Canada/ABCD1233/2023 Eastern Ontario Regional Laboratory Association RespLab@lab.ca Public Health Ontario (PHO) Public Healt Ontario (PHO) 2020-03-18 day Canada Ontario Influenza A virus (H1N1) Not Provided Diagnostic testing Not Provided Swab Saliva;Not Applicable Nasopharynx (NP) Not Applicable Swab Swabbing Homo sapiens Influenza 80 year 80 - 89 Female Baseline surveillance (random sampling) Seasonal flu research project 2023-09-22 Oxford Nanopore MinION Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Porechop 0.2.3 Nanostripper iVar 1.3 95% 400x 100x https://github.com/BCCDC-PHL/nf-flu Tejinder Singh, Fei Hu, Joe Blogs DataHarmonizer v1.9.7, Influenza v1.2.3
6+
prov_fluA_14 A/Ontario/Canada/ABCD1234/2023 Eastern Ontario Regional Laboratory Association RespLab@lab.ca Public Health Ontario (PHO) Public Health Ontario (PHO) 2020-03-19 day Canada Ontario Influenza A virus (H1N1) Not Provided Diagnostic testing Not Provided Swab Saliva;Not Applicable Nasopharynx (NP) Not Applicable Swab Swabbing Homo sapiens Influenza 92 year 90 - 99 Not Provided Baseline surveillance (random sampling) Seasonal flu research project 2019-01-22 Oxford Nanopore MinION Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Porechop 0.2.3 Nanostripper iVar 1.3 95% 400x 100x https://github.com/BCCDC-PHL/nf-flu Tejinder Singh, Fei Hu, Joe Blogs DataHarmonizer v1.9.7, Influenza v1.2.3
7+
prov_fluA_15 A/Ontario/Canada/ABCD1235/2023 Eastern Ontario Regional Laboratory Association RespLab@lab.ca Public Health Ontario (PHO) Public Health Ontario (PHO) 2020-03-22 day Canada Ontario Influenza A virus (H1N1) Not Provided Diagnostic testing Not Provided Swab Saliva;Not Applicable Nasopharynx (NP) Not Applicable Nasopharyngeal swab Swabbing Homo sapiens Influenza 36 year 30 - 39 Not Provided Baseline surveillance (random sampling) Seasonal flu research project 2023-09-22 Oxford Nanopore MinION Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Porechop 0.2.3 Nanostripper iVar 1.3 95% 400x 100x https://github.com/BCCDC-PHL/nf-flu Tejinder Singh, Fei Hu, Joe Blogs DataHarmonizer v1.9.7, Influenza v1.2.3

‎web/templates/influenza/exampleInput/influenza-validTestData_1-2-3.tsv‎

Lines changed: 7 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,7 @@
1+
Database Identifiers Sample collection and processing Host Information Host vaccination information Host exposure information Sequencing Bioinformatics and QC metrics Pathogen diagnostic testing Contributor acknowledgement
2+
specimen collector sample ID third party lab service provider name third party lab sample ID case ID Related specimen primary ID IRIDA sample name umbrella bioproject accession bioproject accession biosample accession SRA accession GenBank accession GISAID accession GISAID virus name sample collected by sample collector contact email sequenced by sequence submitted by sample collection date sample collection date precision geo_loc_name (country) geo_loc_name (state/province/territory) organism isolate ID purpose of sampling purpose of sampling details NML submitted specimen type Related specimen relationship type presampling_activity presampling activity details anatomical material anatomical part body product collection device collection method collection protocol specimen processing specimen processing details biomaterial extracted host (common name) host (scientific name) host health state host health status details host health outcome host disease host age host age unit host age bin host gender host subject ID host vaccination status vaccination history exposure event exposure contact level host role exposure setting exposure details purpose of sequencing purpose of sequencing details sequencing date amplicon size library preparation kit sequencing instrument sequencing protocol amplicon pcr primer scheme raw sequence data processing method dehosting method consensus sequence software name consensus sequence software version breadth of coverage value depth of coverage value depth of coverage threshold number of base pairs sequenced consensus genome length reference genome accession bioinformatics protocol gene name 1 diagnostic pcr Ct value 1 gene name 2 diagnostic pcr Ct value 2 gene name 3 diagnostic pcr Ct value 3 authors DataHarmonizer provenance
3+
prov_fluA_11 Switch Health SHK123456 ABCD1234 SR20-12345 prov_flu_99 PRJNA623807 PRJNA608651 SAMN14180202 SRR11177792 NC_007362.1 EPI_ISL_436489 A/Ontario/Canada/ABCD1231/2023 Eastern Ontario Regional Laboratory Association RespLab@lab.ca Public Health Ontario (PHO) Public Health Ontario (PHO) 2020-03-16 day Canada Ontario Influenza A virus (H1N1) Not Provided Diagnostic testing Not Provided Swab Reinfection testing Vaccination Patient was previously infected. Sample taken during convalescence. Saliva;Not Applicable Nasopharynx (NP) Not Applicable Swab Swabbing FluSamplingProtocol v. 1.2 Virus passage 25 swabs were pooled and further prepared as a single sample during library prep. RNA (total) Human Homo sapiens Symptomatic Hospitalized (ICU) Recovered Influenza 79 year 70 - 79 Male BCxy123 Fully Vaccinated Social Gathering Direct contact (direct human-to-human contact) Inpatient Healthcare Setting Case infected family at home Baseline surveillance (random sampling) Seasonal flu research project 2023-09-22 300bp Nextera XT Oxford Nanopore MinION Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Porechop 0.2.3 Nanostripper iVar 1.3 95% 400x 100x https://github.com/BCCDC-PHL/nf-flu Haemagglutinin (HA) gene 21 Matrix (M) gene 36 Not Applicable Not Applicable Tejinder Singh, Fei Hu, Joe Blogs DataHarmonizer v1.9.7, Influenza v1.2.3
4+
prov_fluA_12 A/Ontario/Canada/ABCD1232/2023 Eastern Ontario Regional Laboratory Association RespLab@lab.ca Public Health Ontario (PHO) Public Health Ontario (PHO) 2020-03-18 day Canada Ontario Influenza A virus (H1N1) Not Provided Diagnostic testing Not Provided Swab Saliva;Not Applicable Nasopharynx (NP) Not Applicable Swab Swabbing Homo sapiens Influenza 54 year 50 - 59 Female Baseline surveillance (random sampling) Seasonal flu research project 2023-09-22 Oxford Nanopore MinION Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Porechop 0.2.3 Nanostripper iVar 1.3 95% 400x 100x https://github.com/BCCDC-PHL/nf-flu Tejinder Singh, Fei Hu, Joe Blogs DataHarmonizer v1.9.7, Influenza v1.2.3
5+
prov_fluA_13 A/Ontario/Canada/ABCD1233/2023 Eastern Ontario Regional Laboratory Association RespLab@lab.ca Public Health Ontario (PHO) Public Health Ontario (PHO) 2020-03-18 day Canada Ontario Influenza A virus (H1N1) Not Provided Diagnostic testing Not Provided Swab Saliva;Not Applicable Nasopharynx (NP) Not Applicable Swab Swabbing Homo sapiens Influenza 80 year 80 - 89 Female Baseline surveillance (random sampling) Seasonal flu research project 2023-09-22 Oxford Nanopore MinION Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Porechop 0.2.3 Nanostripper iVar 1.3 95% 400x 100x https://github.com/BCCDC-PHL/nf-flu Tejinder Singh, Fei Hu, Joe Blogs DataHarmonizer v1.9.7, Influenza v1.2.3
6+
prov_fluA_14 A/Ontario/Canada/ABCD1234/2023 Eastern Ontario Regional Laboratory Association RespLab@lab.ca Public Health Ontario (PHO) Public Health Ontario (PHO) 2020-03-19 day Canada Ontario Influenza A virus (H1N1) Not Provided Diagnostic testing Not Provided Swab Saliva;Not Applicable Nasopharynx (NP) Not Applicable Swab Swabbing Homo sapiens Influenza 92 year 90 - 99 Not Provided Baseline surveillance (random sampling) Seasonal flu research project 2023-09-22 Oxford Nanopore MinION Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Porechop 0.2.3 Nanostripper iVar 1.3 95% 400x 100x https://github.com/BCCDC-PHL/nf-flu Tejinder Singh, Fei Hu, Joe Blogs DataHarmonizer v1.9.7, Influenza v1.2.3
7+
prov_fluA_15 A/Ontario/Canada/ABCD1235/2023 Eastern Ontario Regional Laboratory Association RespLab@lab.ca Public Health Ontario (PHO) Public Health Ontario (PHO) 2020-03-22 day Canada Ontario Influenza A virus (H1N1) Not Provided Diagnostic testing Not Provided Swab Saliva;Not Applicable Nasopharynx (NP) Not Applicable Swab Swabbing Homo sapiens Influenza 36 year 30 - 39 Not Provided Baseline surveillance (random sampling) Seasonal flu research project 2023-09-22 Oxford Nanopore MinION Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Porechop 0.2.3 Nanostripper iVar 1.3 95% 400x 100x https://github.com/BCCDC-PHL/nf-flu Tejinder Singh, Fei Hu, Joe Blogs DataHarmonizer v1.9.7, Influenza v1.2.3

0 commit comments

Comments
 (0)