diff --git a/data/nextstrain/collection.json b/data/nextstrain/collection.json index efe924024..8656862a7 100644 --- a/data/nextstrain/collection.json +++ b/data/nextstrain/collection.json @@ -51,6 +51,7 @@ "nextstrain/flu/h3n2/pa", "nextstrain/flu/h1n1pdm/pb2", "nextstrain/flu/h1n1pdm/pb1", - "nextstrain/flu/h3n2/pb2" + "nextstrain/flu/h3n2/pb2", + "nextstrain/scratch/reference-only" ] } diff --git a/data/nextstrain/scratch/reference-only/CHANGELOG.md b/data/nextstrain/scratch/reference-only/CHANGELOG.md new file mode 100644 index 000000000..0b181e6ea --- /dev/null +++ b/data/nextstrain/scratch/reference-only/CHANGELOG.md @@ -0,0 +1,5 @@ +## Unreleased + +Initial release of this v3 dataset. + +This dataset is new to v3 and does not have a v2 equivalent. diff --git a/data/nextstrain/scratch/reference-only/README.md b/data/nextstrain/scratch/reference-only/README.md new file mode 100644 index 000000000..83cdbb459 --- /dev/null +++ b/data/nextstrain/scratch/reference-only/README.md @@ -0,0 +1,7 @@ +# Scratch dataset for alignment to custom reference + +## Scope of this dataset + +This dataset is a minimal example to allow users to upload their own reference sequence and align some other sequences to that reference. + +To use this dataset, you _must_ upload your own reference sequence in FASTA format, through the "customize" interface. diff --git a/data/nextstrain/scratch/reference-only/examples.fasta b/data/nextstrain/scratch/reference-only/examples.fasta new file mode 100644 index 000000000..4d5416fde --- /dev/null +++ b/data/nextstrain/scratch/reference-only/examples.fasta @@ -0,0 +1,4 @@ +>Demo sequence 1 +ACGTGCGTACGTACGTACGTACGTACGTACGCGTACGTACGTACGTACGTACGTACGTACGTACGTACGTATGTACGTACGTACGTACGTACGTACGTACGTACGNNNGTACGTACGTACGTACGRACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +>Demo sequence 2 +ACGTGCGTACGTACGTACGTACGTACGTACGCGTACGTACGTACGTACGTACGTACGTACGTACGTACGTATGTACGTACGTACGTACGTACGTACGTACGTACGNNNGTACGTACGTACGTACGRACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTANNNNACGTACGTACGTACGTACGTACGTACGTACGTACTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTATACGTACGTACGTACGTACGTACGTACGT diff --git a/data/nextstrain/scratch/reference-only/pathogen.json b/data/nextstrain/scratch/reference-only/pathogen.json new file mode 100644 index 000000000..b9f1b1569 --- /dev/null +++ b/data/nextstrain/scratch/reference-only/pathogen.json @@ -0,0 +1,52 @@ +{ + "alignmentParams": { + "excessBandwidth": 9, + "terminalBandwidth": 100, + "allowedMismatches": 4, + "gapAlignmentSide": "right", + "minSeedCover": 0.1 + }, + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + }, + "files": { + "changelog": "CHANGELOG.md", + "pathogenJson": "pathogen.json", + "readme": "README.md", + "reference": "reference.fasta", + "examples": "examples.fasta" + }, + "schemaVersion": "3.0.0", + "version": { + "tag": "unreleased" + }, + "maintenance": { + "website": [ + "https://nextstrain.org", + "https://clades.nextstrain.org" + ], + "documentation": [ + "https://github.com/nextstrain/nextclade_data", + "https://docs.nextstrain.org/projects/nextclade" + ], + "source code": [ + "https://github.com/nextstrain/nextclade_data", + "https://github.com/neherlab/nextclade_data_workflows" + ], + "issues": [ + "https://github.com/nextstrain/nextclade_data", + "https://github.com/nextstrain/nextclade_data/issues" + ], + "organizations": [ + "Nextstrain" + ], + "authors": [ + "Nextstrain team " + ] + }, + "attributes": { + "name": "Scratch - Reference only", + "reference name": "None - Bring your own" + } +} diff --git a/data/nextstrain/scratch/reference-only/reference.fasta b/data/nextstrain/scratch/reference-only/reference.fasta new file mode 100644 index 000000000..1b517a082 --- /dev/null +++ b/data/nextstrain/scratch/reference-only/reference.fasta @@ -0,0 +1,2 @@ +>Placeholder +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT diff --git a/data_output/index.json b/data_output/index.json index 8a2f38a5d..483820894 100644 --- a/data_output/index.json +++ b/data_output/index.json @@ -2015,6 +2015,61 @@ "web": "3.0.0-alpha.0" } } + }, + { + "path": "nextstrain/scratch/reference-only", + "enabled": true, + "attributes": { + "name": "Scratch - Reference only", + "reference name": "None - Bring your own" + }, + "maintenance": { + "website": [ + "https://nextstrain.org", + "https://clades.nextstrain.org" + ], + "documentation": [ + "https://github.com/nextstrain/nextclade_data", + "https://docs.nextstrain.org/projects/nextclade" + ], + "source code": [ + "https://github.com/nextstrain/nextclade_data", + "https://github.com/neherlab/nextclade_data_workflows" + ], + "issues": [ + "https://github.com/nextstrain/nextclade_data", + "https://github.com/nextstrain/nextclade_data/issues" + ], + "organizations": [ + "Nextstrain" + ], + "authors": [ + "Nextstrain team " + ] + }, + "files": { + "changelog": "CHANGELOG.md", + "pathogenJson": "pathogen.json", + "readme": "README.md", + "reference": "reference.fasta", + "examples": "examples.fasta" + }, + "versions": [ + { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + } + ], + "version": { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + } } ] }, diff --git a/data_output/minimizer_index.json b/data_output/minimizer_index.json index 37d119429..0099fa654 100644 --- a/data_output/minimizer_index.json +++ b/data_output/minimizer_index.json @@ -84110,190 +84110,196 @@ { "name": "nextstrain/flu/h1n1pdm/ha/CY121680", "length": 1752, - "nMinimizers": 113 + "nMinimizers": 114 }, { "name": "nextstrain/flu/h1n1pdm/ha/MW626062", "length": 1752, - "nMinimizers": 116 + "nMinimizers": 117 }, { "name": "nextstrain/flu/h1n1pdm/mp", "length": 982, - "nMinimizers": 63 + "nMinimizers": 64 }, { "name": "nextstrain/flu/h1n1pdm/na/MW626056", "length": 1433, - "nMinimizers": 71 + "nMinimizers": 72 }, { "name": "nextstrain/flu/h1n1pdm/np", "length": 1497, - "nMinimizers": 100 + "nMinimizers": 101 }, { "name": "nextstrain/flu/h1n1pdm/ns", "length": 863, - "nMinimizers": 73 + "nMinimizers": 74 }, { "name": "nextstrain/flu/h1n1pdm/pa", "length": 2151, - "nMinimizers": 137 + "nMinimizers": 138 }, { "name": "nextstrain/flu/h1n1pdm/pb1", "length": 2274, - "nMinimizers": 142 + "nMinimizers": 143 }, { "name": "nextstrain/flu/h1n1pdm/pb2", "length": 2280, - "nMinimizers": 132 + "nMinimizers": 133 }, { "name": "nextstrain/flu/h3n2/ha/CY163680", "length": 1737, - "nMinimizers": 105 + "nMinimizers": 106 }, { "name": "nextstrain/flu/h3n2/ha/EPI1857216", "length": 1718, - "nMinimizers": 100 + "nMinimizers": 101 }, { "name": "nextstrain/flu/h3n2/mp", "length": 1027, - "nMinimizers": 71 + "nMinimizers": 72 }, { "name": "nextstrain/flu/h3n2/na/EPI1857215", "length": 1439, - "nMinimizers": 95 + "nMinimizers": 96 }, { "name": "nextstrain/flu/h3n2/np", "length": 1566, - "nMinimizers": 94 + "nMinimizers": 95 }, { "name": "nextstrain/flu/h3n2/ns", "length": 890, - "nMinimizers": 50 + "nMinimizers": 51 }, { "name": "nextstrain/flu/h3n2/pa", "length": 2233, - "nMinimizers": 148 + "nMinimizers": 149 }, { "name": "nextstrain/flu/h3n2/pb1", "length": 2341, - "nMinimizers": 140 + "nMinimizers": 141 }, { "name": "nextstrain/flu/h3n2/pb2", "length": 2341, - "nMinimizers": 121 + "nMinimizers": 122 }, { "name": "nextstrain/flu/vic/ha/KX058884", "length": 1885, - "nMinimizers": 117 + "nMinimizers": 118 }, { "name": "nextstrain/flu/vic/na/CY073894", "length": 1401, - "nMinimizers": 90 + "nMinimizers": 91 }, { "name": "nextstrain/flu/yam/ha/JN993010", "length": 1755, - "nMinimizers": 111 + "nMinimizers": 112 }, { "name": "nextstrain/mpox/all-clades", "length": 197209, - "nMinimizers": 12012 + "nMinimizers": 12013 }, { "name": "nextstrain/mpox/clade-iib", "length": 197209, - "nMinimizers": 12012 + "nMinimizers": 12013 }, { "name": "nextstrain/mpox/lineage-b.1", "length": 197209, - "nMinimizers": 12020 + "nMinimizers": 12021 }, { "name": "nextstrain/rsv/a/EPI_ISL_412866", "length": 15225, - "nMinimizers": 976 + "nMinimizers": 977 }, { "name": "nextstrain/rsv/b/EPI_ISL_1653999", "length": 15222, - "nMinimizers": 935 + "nMinimizers": 936 }, { "name": "nextstrain/sars-cov-2/BA.2", "length": 29903, - "nMinimizers": 1849 + "nMinimizers": 1850 }, { "name": "nextstrain/sars-cov-2/BA.2.86", "length": 29903, - "nMinimizers": 1839 + "nMinimizers": 1840 }, { "name": "nextstrain/sars-cov-2/XBB", "length": 29903, - "nMinimizers": 1835 + "nMinimizers": 1836 }, { "name": "nextstrain/sars-cov-2/wuhan-hu-1/orfs", "length": 29903, - "nMinimizers": 1853 + "nMinimizers": 1854 }, { "name": "nextstrain/sars-cov-2/wuhan-hu-1/proteins", "length": 29903, - "nMinimizers": 1853 + "nMinimizers": 1854 + }, + { + "name": "nextstrain/scratch/reference-only", + "length": 1728, + "nMinimizers": 1 } ], "normalization": [ - 15.504424778761061, - 15.10344827586207, - 15.587301587301587, - 20.183098591549296, - 14.97, - 11.821917808219178, - 15.700729927007298, - 16.014084507042252, - 17.272727272727273, - 16.542857142857144, - 17.18, - 14.464788732394366, - 15.147368421052631, - 16.659574468085108, - 17.8, - 15.087837837837839, - 16.72142857142857, - 19.34710743801653, - 16.11111111111111, - 15.566666666666666, - 15.81081081081081, - 16.417665667665666, - 16.417665667665666, - 16.406738768718803, - 15.59938524590164, - 16.280213903743316, - 16.172525689561926, - 16.26046764545949, - 16.29591280653951, - 16.137614678899084, - 16.137614678899084 + 15.368421052631579, + 14.974358974358974, + 15.34375, + 19.90277777777778, + 14.821782178217822, + 11.662162162162161, + 15.58695652173913, + 15.902097902097902, + 17.142857142857142, + 16.38679245283019, + 17.00990099009901, + 14.26388888888889, + 14.989583333333334, + 16.48421052631579, + 17.45098039215686, + 14.986577181208053, + 16.602836879432623, + 19.188524590163933, + 15.974576271186441, + 15.395604395604396, + 15.669642857142858, + 16.416299009406476, + 16.416299009406476, + 16.40537392895766, + 15.583418628454453, + 16.262820512820515, + 16.163783783783785, + 16.25163043478261, + 16.287037037037038, + 16.12891046386192, + 16.12891046386192, + 1728.0 ] } diff --git a/data_output/nextstrain/scratch/reference-only/unreleased/CHANGELOG.md b/data_output/nextstrain/scratch/reference-only/unreleased/CHANGELOG.md new file mode 100644 index 000000000..0b181e6ea --- /dev/null +++ b/data_output/nextstrain/scratch/reference-only/unreleased/CHANGELOG.md @@ -0,0 +1,5 @@ +## Unreleased + +Initial release of this v3 dataset. + +This dataset is new to v3 and does not have a v2 equivalent. diff --git a/data_output/nextstrain/scratch/reference-only/unreleased/README.md b/data_output/nextstrain/scratch/reference-only/unreleased/README.md new file mode 100644 index 000000000..83cdbb459 --- /dev/null +++ b/data_output/nextstrain/scratch/reference-only/unreleased/README.md @@ -0,0 +1,7 @@ +# Scratch dataset for alignment to custom reference + +## Scope of this dataset + +This dataset is a minimal example to allow users to upload their own reference sequence and align some other sequences to that reference. + +To use this dataset, you _must_ upload your own reference sequence in FASTA format, through the "customize" interface. diff --git a/data_output/nextstrain/scratch/reference-only/unreleased/examples.fasta b/data_output/nextstrain/scratch/reference-only/unreleased/examples.fasta new file mode 100644 index 000000000..4d5416fde --- /dev/null +++ b/data_output/nextstrain/scratch/reference-only/unreleased/examples.fasta @@ -0,0 +1,4 @@ +>Demo sequence 1 +ACGTGCGTACGTACGTACGTACGTACGTACGCGTACGTACGTACGTACGTACGTACGTACGTACGTACGTATGTACGTACGTACGTACGTACGTACGTACGTACGNNNGTACGTACGTACGTACGRACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +>Demo sequence 2 +ACGTGCGTACGTACGTACGTACGTACGTACGCGTACGTACGTACGTACGTACGTACGTACGTACGTACGTATGTACGTACGTACGTACGTACGTACGTACGTACGNNNGTACGTACGTACGTACGRACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTANNNNACGTACGTACGTACGTACGTACGTACGTACGTACTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTATACGTACGTACGTACGTACGTACGTACGT diff --git a/data_output/nextstrain/scratch/reference-only/unreleased/pathogen.json b/data_output/nextstrain/scratch/reference-only/unreleased/pathogen.json new file mode 100644 index 000000000..b9f1b1569 --- /dev/null +++ b/data_output/nextstrain/scratch/reference-only/unreleased/pathogen.json @@ -0,0 +1,52 @@ +{ + "alignmentParams": { + "excessBandwidth": 9, + "terminalBandwidth": 100, + "allowedMismatches": 4, + "gapAlignmentSide": "right", + "minSeedCover": 0.1 + }, + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + }, + "files": { + "changelog": "CHANGELOG.md", + "pathogenJson": "pathogen.json", + "readme": "README.md", + "reference": "reference.fasta", + "examples": "examples.fasta" + }, + "schemaVersion": "3.0.0", + "version": { + "tag": "unreleased" + }, + "maintenance": { + "website": [ + "https://nextstrain.org", + "https://clades.nextstrain.org" + ], + "documentation": [ + "https://github.com/nextstrain/nextclade_data", + "https://docs.nextstrain.org/projects/nextclade" + ], + "source code": [ + "https://github.com/nextstrain/nextclade_data", + "https://github.com/neherlab/nextclade_data_workflows" + ], + "issues": [ + "https://github.com/nextstrain/nextclade_data", + "https://github.com/nextstrain/nextclade_data/issues" + ], + "organizations": [ + "Nextstrain" + ], + "authors": [ + "Nextstrain team " + ] + }, + "attributes": { + "name": "Scratch - Reference only", + "reference name": "None - Bring your own" + } +} diff --git a/data_output/nextstrain/scratch/reference-only/unreleased/reference.fasta b/data_output/nextstrain/scratch/reference-only/unreleased/reference.fasta new file mode 100644 index 000000000..1b517a082 --- /dev/null +++ b/data_output/nextstrain/scratch/reference-only/unreleased/reference.fasta @@ -0,0 +1,2 @@ +>Placeholder +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT diff --git a/scripts/lib/minimizer.py b/scripts/lib/minimizer.py index aea4b3f88..fb5a2c481 100644 --- a/scripts/lib/minimizer.py +++ b/scripts/lib/minimizer.py @@ -71,7 +71,7 @@ def make_ref_search_index(refs): "meta": { "name": name, "length": len(ref.seq), - "nMinimizers": len(minimizers) + "nMinimizers": len(minimizers) + 1 # +1 to not divide by zero } })