Add simple influenza A H5N1 dataset with all segments

.gitignore

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 \.env
 \.vscode
 /docs/tmp/
+\.venv

data/community/genspectrum/iav/h5n1/GG1996/HA/CHANGELOG.md

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+## Unreleased
+
+Initial release

data/community/genspectrum/iav/h5n1/GG1996/HA/README.md

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+# H5N1 (segment4/ HA) - dataset with A/Goose/Guangdong/1/96 reference
+
+| attribute           | value                                    |
+| ------------------- | ---------------------------------------- |
+| dataset name        | community/genspectrum/iav/h5n1/GG1996/HA |
+| reference strain    | A/Goose/Guangdong/1/96(H5N1)             |
+| reference accession | NC_007362.1                              |
+| assembly accession  | GCF_000864105.1                          |
+
+## Authors and contacts
+
+Maintained by Genspectrum, Chaoran Chen and Anna Parker
+
+With the help of: Cornelius Roemer and Richard Neher
+
+## Scope of this dataset
+
+This dataset uses the first highly-pathogenic avian influenza (HPAI) isolate (A/Goose/Guangdong/1/96) as a reference and is suitable for the analysis of circulating and historical H5 sequences, including low-pathogenicity avian influenza (LPAI) isolates.
+
+## Features
+
+This simple dataset only supports alignment.
+
+## What is Nextclade dataset
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/community/genspectrum/iav/h5n1/GG1996/HA/genome_annotation.gff3

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+.	.	CDS	22	1728	.	+	.	gene="HA"

data/community/genspectrum/iav/h5n1/GG1996/HA/pathogen.json

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+{
+  "schemaVersion": "3.0.0",
+  "alignmentParams": {
+    "minSeedCover": 0.01
+  },
+  "attributes": {
+    "name": "Influenza A/H5N1 (segment 4/HA)",
+    "reference name": "Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) hemagglutinin (HA) gene, complete cds",
+    "reference accession": "NC_007362.1"
+  },
+  "files": {
+    "reference": "reference.fasta",
+    "pathogenJson": "pathogen.json",
+    "changelog": "CHANGELOG.md",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "readme": "README.md",
+    "examples": "examples.fasta"
+  }
+}

data/community/genspectrum/iav/h5n1/GG1996/HA/reference.fasta

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+>NC_007362.1 Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) hemagglutinin (HA) gene, complete cds
+GCAGGGGTATAATCTGTCAAAATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTCAAAAGTG
+ATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGT
+TACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAATGGGAAGCTCTGCGATCTAAATGGAGTG
+AAGCCTCTCATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTGACGAATTCA
+TCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGA
+TTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAACAAACCATTTTGAGAAAATTCAGATCATC
+CCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCATGGGAGGT
+CCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTA
+CAATAATACCAACCAAGAAGATCTTTTAGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAG
+ACAAAGCTCTATCAAAACCCAACCACTTACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTC
+CAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAA
+GCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTC
+AAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTC
+CAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCCAA
+ATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAGAGAGAGAGAAGAAGA
+AAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTT
+GGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGC
+AATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGA
+AGGGAATTTAATAACTTGGAAAGGAGGATAGAGAATTTAAACAAGCAGATGGAAGACGGATTCCTAGATG
+TCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAA
+TGTCAAGAACCTTTATGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAATGGTTGT
+TTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGC
+AGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTA
+CCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCT
+TTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATTTAAATTTGTGAGTTCAGATTGTAGT
+TAAAAACACC

data/community/genspectrum/iav/h5n1/GG1996/M/CHANGELOG.md

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+## Unreleased
+
+Initial release

data/community/genspectrum/iav/h5n1/GG1996/M/README.md

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+# H5N1 (segment7/ M) - dataset with A/Goose/Guangdong/1/96 reference
+
+| attribute           | value                                   |
+| ------------------- | --------------------------------------- |
+| dataset name        | community/genspectrum/iav/h5n1/GG1996/M |
+| reference strain    | A/Goose/Guangdong/1/96(H5N1)            |
+| reference accession | NC_007363.1                             |
+| assembly accession  | GCF_000864105.1                         |
+
+## Authors and contacts
+
+Maintained by Genspectrum, Chaoran Chen and Anna Parker
+
+With the help of: Cornelius Roemer and Richard Neher
+
+## Scope of this dataset
+
+This dataset uses the first highly-pathogenic avian influenza (HPAI) isolate (A/Goose/Guangdong/1/96) as a reference and is suitable for the analysis of circulating and historical H5 sequences, including low-pathogenicity avian influenza (LPAI) isolates.
+
+## Features
+
+This simple dataset only supports alignment.
+
+## What is Nextclade dataset
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/community/genspectrum/iav/h5n1/GG1996/M/genome_annotation.gff3

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+.	.	CDS	26	784	.	+	.	gene="M1"
+.	.	gene	26	1007	.	+	.	gene=M2;ID=gene-M2
+.	.	CDS	26	51	.	+	.	gene=M2;ID=cds-M2;Parent=gene-M2
+.	.	CDS	740	1007	.	+	.	gene=M2;ID=cds-M2;Parent=gene-M2

data/community/genspectrum/iav/h5n1/GG1996/M/pathogen.json

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+{
+  "schemaVersion": "3.0.0",
+  "alignmentParams": {
+    "minSeedCover": 0.01
+  },
+  "attributes": {
+    "name": "Influenza A/H5N1 (segment 7/M)",
+    "reference name": "Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) segment 7, complete sequence",
+    "reference accession": "NC_007363.1"
+  },
+  "files": {
+    "reference": "reference.fasta",
+    "pathogenJson": "pathogen.json",
+    "changelog": "CHANGELOG.md",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "readme": "README.md",
+    "examples": "examples.fasta"
+  }
+}

data/community/genspectrum/iav/h5n1/GG1996/M/reference.fasta

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+>NC_007363.1 Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) segment 7, complete sequence
+AGCAAAAGCAGGTAGATATTGAAAAATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCGTC
+CCGTCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAGGATGTCTTTGCAGGAAAGAACACCGATC
+TCGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAAGGGATTTTAGGATT
+TGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAGAATGCCTTAAAT
+GGAAATGGAGATCCAAACAATATGGATAGGGCAGTTAAGCTATACAAGAAGCTGAAAAGAGAAATAACAT
+TCCATGGGGCTAAGGAGGTCGCACTCAGCTACTCAACCGGTGCACTTGCCAGTTGTATGGGTCTCATATA
+CAACAGGATGGGAACGGTGACCACAGAAGTGGCTTTTGGCCTAGTGTGTGCCACTTGTGAGCAGATTGCA
+GATTCACAGCATCGGTCTCACAGACAGATGGCAACTACCACCAACCCACTAATCAGGCATGAGAACAGAA
+TGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCTGGATCGAGTGAGCAGGCAGCGGAAGC
+CATGGAGGTTGCTAGTCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAGCTCC
+AGTGCCGGTCTGAAAGATAATCTTCTTGAAAATTTGCAGGCCTACCAAAAACGAATGGGAGTGCAAATGC
+AGCGATTCAAGTGATCCTCTTGTTGTTGCCGCAAGTATCATTGGGATACTGCACTTGATATTGTGGATTC
+TTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGA
+AGGGGTACCTGAGTCTATGAGGGAAGAGTATCGGCAGGAACAGCAGAGTGCTGTGGATGTTGACGATGGT
+CATTTTGTCAACATAGAGCTGGAGTAAAAAACTACCTTGTTTCTACT

data/community/genspectrum/iav/h5n1/GG1996/NA/CHANGELOG.md

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+## Unreleased
+
+Initial release

data/community/genspectrum/iav/h5n1/GG1996/NA/README.md

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+# H5N1 (segment6/ NA) - dataset with A/Goose/Guangdong/1/96 reference
+
+| attribute           | value                                    |
+| ------------------- | ---------------------------------------- |
+| dataset name        | community/genspectrum/iav/h5n1/GG1996/NA |
+| reference strain    | A/Goose/Guangdong/1/96(H5N1)             |
+| reference accession | NC_007361.1                              |
+| assembly accession  | GCF_000864105.1                          |
+
+## Authors and contacts
+
+Maintained by Genspectrum, Chaoran Chen and Anna Parker
+
+With the help of: Cornelius Roemer and Richard Neher
+
+## Scope of this dataset
+
+This dataset uses the first highly-pathogenic avian influenza (HPAI) isolate (A/Goose/Guangdong/1/96) as a reference and is suitable for the analysis of circulating and historical H5 sequences, including low-pathogenicity avian influenza (LPAI) isolates.
+
+## Features
+
+This simple dataset only supports alignment.
+
+## What is Nextclade dataset
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html