Artic flu a

primerschemes/artic-flu-a/800/v1.0.0/README.md

@@ -0,0 +1,64 @@
+# artic-flu-a 800bp v1.0.0
+
+[![Generic badge](https://img.shields.io/badge/STATUS-draft-blue.svg)](https://labs.primalscheme.com/faqs)
+
+[primalscheme labs](https://labs.primalscheme.com/detail/artic-flu-a/800/v1.0.0)
+
+## Description
+
+PrimerScheme for influenza A utilising tuni-primers alongside internal-primers for larger segments
+
+## Overviews
+
+![pa_1934_Avian_A_chicken_Germany_1934_Germany_H7N1.png](work/pa_1934_Avian_A_chicken_Germany_1934_Germany_H7N1.png)
+
+![pb1_1934_Avian_A_chicken_Germany_1934_Germany_H7N1.png](work/pb1_1934_Avian_A_chicken_Germany_1934_Germany_H7N1.png)
+
+![pb2_1934_Avian_A_chicken_Rostock_45_1934_Germany_H7N1.png](work/pb2_1934_Avian_A_chicken_Rostock_45_1934_Germany_H7N1.png)
+
+## Details
+
+```json
+{
+    "ampliconsize": 800,
+    "schemeversion": "v1.0.0",
+    "schemename": "artic-flu-a",
+    "primer_bed_md5": "3a01f111d4223a265a2fa20e4e26a349",
+    "reference_fasta_md5": "b5490b7015ab4cf2b552d18904350cab",
+    "status": "draft",
+    "citations": [],
+    "authors": [
+        "artic-network"
+    ],
+    "algorithmversion": "primalscheme3.2.0-artic-flu",
+    "species": [
+        11320
+    ],
+    "license": "CC BY-SA 4.0",
+    "primerclass": "primerschemes",
+    "infoschema": "v2.1.0",
+    "articbedversion": "v3.0",
+    "collections": [
+        "ARTIC"
+    ],
+    "links": {
+        "protocols": [],
+        "validation": [],
+        "homepage": [],
+        "vendors": [],
+        "misc": []
+    },
+    "refselect": null,
+    "description": "PrimerScheme for influenza A utilising tuni-primers alongside internal-primers for larger segments",
+    "derivedfrom": null,
+    "contactinfo": null
+}
+```
+
+
+
+------------------------------------------------------------------------
+
+This work is licensed under a [Creative Commons Attribution-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-sa/4.0/) 
+
+![](https://i.creativecommons.org/l/by-sa/4.0/88x31.png)

primerschemes/artic-flu-a/800/v1.0.0/info.json

@@ -0,0 +1,34 @@
+{
+    "ampliconsize": 800,
+    "schemeversion": "v1.0.0",
+    "schemename": "artic-flu-a",
+    "primer_bed_md5": "3a01f111d4223a265a2fa20e4e26a349",
+    "reference_fasta_md5": "b5490b7015ab4cf2b552d18904350cab",
+    "status": "draft",
+    "citations": [],
+    "authors": [
+        "artic-network"
+    ],
+    "algorithmversion": "primalscheme3.2.0-artic-flu",
+    "species": [
+        11320
+    ],
+    "license": "CC BY-SA 4.0",
+    "primerclass": "primerschemes",
+    "infoschema": "v2.1.0",
+    "articbedversion": "v3.0",
+    "collections": [
+        "ARTIC"
+    ],
+    "links": {
+        "protocols": [],
+        "validation": [],
+        "homepage": [],
+        "vendors": [],
+        "misc": []
+    },
+    "refselect": null,
+    "description": "PrimerScheme for influenza A utilising tuni-primers alongside internal-primers for larger segments",
+    "derivedfrom": null,
+    "contactinfo": null
+}

primerschemes/artic-flu-a/800/v1.0.0/reference.fasta

@@ -0,0 +1,230 @@
+>pa_1934_Avian_A_chicken_Germany_1934_Germany_H7N1
+ATGGAAGAATTTGTGCGACAATGCTTCAATCCAATGATCGTCGAGCTTGCGGAAAAGACA
+ATGAAAGAATATGGAGAGGACCCGAAGATTGAAACAAACAAATTCGCCGCAATATGCACA
+CATTTGGAAGTGTGTTTCATGTATTCAGATTTCCACTTTATTGATGAACGGGGAGAGTCA
+ATGATTGTAGAATCTGGTGACCCAAATGCACTCTTGAAGCACCGATTTGAGATAATTGAA
+GGAAGAGATCGCACGATGGCCTGGACGGTGGTGAATAGCATTTGCAATACTACAGGGGTT
+GAGAAACCCAAGTTCCTTCCGGATTTGTATGATTATAAGGAGAACCGATTCATTGAAATT
+GGAGTGACAAGAAGGGAGGTCCACATATACTACTTAGAAAAAGCCAATAAGATAAAATCT
+GAGAAGACACACATCCACATCTTCTCATTCACTGGGGAAGAAATGGCCACTAAGGCGGAC
+TACACTCTTGATGAAGAGAGCAGAGCAAGGATCAAAACCAGGCTATTCACCATAAGACAA
+GAAATGGCCAGTAGAGGCCTCTGGGATTCCTTTCGTCAGTCCGAGAGAGGCGAAGAGACA
+ATTGAAGAAAGATTTGAAATCACAGGAACCATGCGCAGGCTTGCCGAACAAAGTCTCCCA
+CCGAACTTCTCCAGCCTTGAAAACTTTAGAGCCTATGTGGATGGATTCAAACCGAACGGC
+TGCATTGAGGGCAAGCTTTCTCAAATGTCCAAAGAAGTAAATGCAAGAATCGAGCCATTC
+TTGAAGACAACACCACGCCCTCTCAGATTACCTGATGGGCCTCCCTGTTCTCAGCGGTCA
+AAATTCCTACTGATGGATGCTCTGAAATTAAGCATTGAAGACCCAAGTCATGAGGGGGAG
+GGGATACCACTACATGATGCAATCAAATGCATGAAGACATTTTTTGGCTGGAAAGAGCCC
+AATATTGTCAAACCGCATGAGAAGGGCATAAATCCCAACTATCTCCTGGCTTGGAACCAG
+GTGCTAGCAGAACTGAAGGATATTGAGAATGAGGAGAAAATTCCAAAAACAAAAAACATG
+AAGAAAACAAGCCAGTTAAAGTGGGCACTTGGTGAGAACATGGCACCAGAGAAAGTAGAC
+TTTGAGGATTGCAAGGACATTAGCGATCTGAAGCAGTATGACAGTGATGAGCCAGAACAG
+AGATCACTAGCGAGTTGGATCCAGAGTGAATTCAACAAAGCATGTGAGCTGACCGATTCA
+GGTTGGATAGAACTTGATGAAATAGGAGAAGATGTAGCCCCAATCGAGCACATTGCAAGT
+ATGAGGAGAAACTATTTCACAGCGGAAGTGTCTCACTGCAGGGCAACGGAGTACATAATG
+AAAGGGGTATACATAAACACGGCCTTGCTCAATGCATCTTGTGCAGCTATGGATGACTTC
+CAGCTGATCCCAATGATAAGCAAATGCAGGACCAAAGAAGGAAGACGGAAGACGAATCTG
+TATGGATTCATTATAAAAGGAAGATCTCACTTGAGGAATGATACTGATGTGGTGAATTTT
+GTGAGCATGGAGTTCTCTCTCACTGACCCGAGGCTTGAGCCACACAAGTGGGAGAAGTAT
+TGTGTTCTTGAAATAGGAGACATGCTCCTGCGGACTGCAATAGGCCAAGTATCAAGGCCC
+ATGTTCCTGTATGTGAGAACCAATGGAACCTCCAAAATCAAGATGAAATGGGGTATGGAG
+ATGAGACGTTGCCTTCTTCAGTCCCTTCAACAGGTTGAAAGCATGGTTGAGGCTGAGTCC
+TCTGTCAAGGAGAAAGACATGACTAAAGAATTCTTTGAAAACAAGTCAGAGACGTGGCCC
+ATTGGAGAATCACCTAAAGGAGTGGAAGAAGGTTCCATCGGGAAAGTGTGCAGGACCTTA
+CTGGCGAAGTCTGTATTTAACAGCTTATATGCATCCCCACAACTTGAGGGATTTTCAGCG
+GAATCGAGAAAACTGCTCCTCATTGTTCAGGCTCTTAGAGACAACCTGGAACCTGGAACC
+TTCGATCTTGGAGGGCTATATGGAGCAATTGAGGAGTGCCTGATTAATGATCCCTGGGTT
+TTGCTTAATGCATCTTGGTTCAACTCCTTCCTCACACATGCACTGAAATAG
+>pb1_1934_Avian_A_chicken_Germany_1934_Germany_H7N1
+ATGGATGTCAACCCGACTTTACTTTTCTTAAAAGTTCCAGCGCAAAATGCCATAAGTACT
+ACATTCCCTTACACTGGAGACCCTCCATACAGCCATGGAACGGGAACAGGGTACACCATG
+GACACAGTTAATAGGACACACCAATATTCAGAAAAGGGGAAATGGACAGCAAACACGGAG
+ACTGGAGCACCCCAACTCAACCCAATTGATGGACCACTACCTGAGGACAATGAGCCAAGT
+GGATATGCACAGACAGACTGCGTCCTGGAGGCAATGGCTTTCCTTGAAGAGTCTCACCCC
+GGAATCTTTGAAAACTCATGTCTTGAGACGATGGAAGCTGTTCAGCAAACAAGAGTAGAC
+AAACTGACCCAAGGTCGTCAGACCTATGATTGGACATTGAACAGAAACCAGCCGGCTGCA
+ACTGCATTAGCTAACACTATAGAAGTTTTTAGATCGAATGGTCTGACAGCTAATGAATCA
+GGGAGGCTCATAGATTTCCTCAAGGATGTAATGGAATCGATGGATAAAGAGGAAATGGAG
+ATAACAACACATTTCCAACGAAAAAGAAGAGTAAGAGACAACATGACCAAGAAAATGGTC
+ACACAGAGGACAATAGGGAAGAAGAAGCAGAGGCTAAATAAAAGGAGTTACCTAATAAGA
+GCACTAACATTGAACACAATGACGAAAGATGCAGAAAGAGGTAAACTAAAGAGGCGAGCA
+ATTGCAACACCAGGAATGCAGATCAGGGGGTTTGTGTACTCTGTCGAAACACTGGCAAGG
+AGCATCTGTGAAAAGCTTGAACAGTCTGGGCTACCAGTTGGAGGGAATGAGAAGAAGGCT
+AAGTTGGCGAATGTTGTAAGGAAGATGATGACGAACTCGCAAGACACAGAGCTCTCTTTC
+ACAATCACTGGAGACAATACCAAATGGAATGAGAATCAAAATCCTCGGATGTTCCTGGCA
+ATGATAACATACATCACAAGAAATCAACCTGAATGGTTTAGAAACGTTCTAAGCATCGCA
+CCAATAATGTTCTCAAACAAAATGGCGAGACTAGGGAAGGGGTACATGTTTGAAAGCAAG
+AGTATGAAGCTCCGAACACAAATACCAGCAGAAATGCTAGCAAGTATTGATCTAAAATAC
+TTCAATGAATCAACAAGAAAGAAAATCGAGAAAATAAGGCCCCTCCTAATAGATGGTACC
+GCCTCATTGAGCCCTGGAATGATGATGGGCATGTTTAACATGCTGAGCACGGTATTGGGA
+GTCTCAATTCTGAATCTTGGACAAAAGAGATACACCAAAACCACATACTGGTGGGATGGG
+CTTCAGTCCTCTGATGATTTTGCCCTCATAGTGAATGCACCAAATCATGAGGGAATACAA
+GCGGGAGTGGATAGATTTTACAGGACTTGCAAGCTAGTTGGAATCAATATGAGCAAGAAA
+AAGTCCTATATAAATAGGACAGGGACATTTGAATTCACAAGCTTTTTCTACCGCTATGGA
+TTTGTAGCCAATTTCAGCATGGAGTTGCCCAGTTTTGGGGTGTCCGGGATTAATGAATCA
+GCTGACATGAGCATCGGAGTAACAGTAATAAAGAACAACATGATAAACAACGATCTTGGA
+CCAGCAACAGCCCAGATGGCTCTTCAATTGTTTATCAAGGATTACAGATACACATATCGG
+TGTCACAGGGGAGACACACAAATTCAGACGAGGAGATCATTCGAGCTGAAGAAGCTTTGG
+GAGCAAACCCGCTCAAAGGCTGGGCTGTTGGTTTCAGACGGAGGACCAAACCTATACAAC
+ATTCGGAATCTCCACATTCCGGAAGTCTGTTTAAAGTGGGAACTTATGGATGAAGATTAC
+CAGGGAAGGCTCTGCAATCCCCTGAATCCATTTGTCAGTCACAAAGAAATTGAATCTGTA
+AACAATGCTGTAGTAATGCCAGCCCATGGTCCGGCCAAGAGCACGGAGTATGACGCTGTG
+GCAACTACACACTCCTGGATTCCTAAGAGAAATCGCTCCATTCTTAACACGAGCCAAAGG
+GGCATTCTTGAAGATGAACAAATGTATCAGAAGTGCTGCAACCTATTCGAGAAATTCTTC
+CCTAGCAGTTCATACAGGAGGCCGGTTGGAATTTCCAGTATGGTGGAGGCCATGGTGTCT
+AGGGCCCGAATTGATGCACGAATTGACTTCGAGTCTGGAAGGATTAAGAAGGAAGAGTTT
+GCTGAGATCATGAAAATCTGTTCCACCATTGAAGAGCTCAGACGGCAGAAATAG
+>pb2_1934_Avian_A_chicken_Rostock_45_1934_Germany_H7N1
+ATGGAGAGAATAAAAGAACTAAGAGATTTAATGTCACAGTCTCGCACCCGCGAGATACTC
+ACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAATACACATCCGGAAGACAGGAG
+AAGAACCCTGCCCTCAGAATGAAATGGATGATGGCAATGAAATACCCAATCACAGCAGAC
+AAGAGGATAATAGAAATGATTCCTGAAAAGAATGAACAAGGGCAGACGCTCTGGAGTAAA
+ACAAATGATGCTGGGTCAGACCGGGTAATGGTATCACCTCTTGCTGTAACATGGTGGAAC
+AGAAATGGGCCAACAACAAGTACAGTCCATTACCCAAAGGTTTACAAAACCTACTTTGAA
+AAAGTTGAAAGGTTGAAGCATGGAACCTTCGGCCCTGTCCACTTCCGAAACCAAGTCAAA
+ATACGTCGCAGGGTTGATATAAACCCTGGCCATGCAAATCTCAGTGCTAAAGAGGCACAA
+GATGTCATCATGGAGGTCGTTTTCCCAAATGAAGTGGGAGCCAGGATACTAACATCAGAA
+TCACAATTAACAATAACAAGAGAAAAGAAGGAAGAACTTCAGGACTGTAAAATTGCCCCC
+TTAATGGTGGCATACATGTTGGAAAGAGAACTGGTTCGCAAGACCAGATTTCTCCCAGTG
+GCTGGAGGAACAAGCAGTGTATACATCGAAGTATTGCATTTGACTCAAGGGACCTGCTGG
+GAACAAATGTACACTCCAGGTGGAGAAGTGAGAAACGATGATGTTGATCAGAGCTTGATC
+ATTGCTGCTAGGAACATAGTTAGGAGAGCAACAGTGTCAGCAGACCCACTGGCATCACTG
+TTGGAGATGTGTCATAGCACACAAATTGGTGGGATAAAGATGGTAGACATCCTTAGACAA
+AATCCAACGGAAGAACAAGCCGTGGATATATGCAAGGCGGCAATGGGTTTGAGGATCAGC
+TCATCATTCAGCTTTGGAGGCTTCACTTTCAAAAGAACAAGTGGATCATCTGTCAACAGG
+AAAGAGGAAGTGCTTACGGGCAACCTCCAAACACTGAAAATAAGAGTACATGAAGGATAT
+GAGGAATTCACAATGGTTGGGCGGAGAGCAACAGCTATCCTAAGGAAAGCAACCAGAAGG
+CTGATTCAGCTGATAGTAAGTGGAAGAGACGAACAGTCAATCGCTGAAGCAGTCATTGTA
+GCGATGGTGTTTTCACAAGAAGATTGTATGATAAAAGCAGTCCGAGGTGATCTGAACTTC
+GTGAACAGAGCGAACCAGCGGCTGAATCCCATGCACCAACTTTTGAGACACTTCCAAAAA
+GATGCAAAAACGTTATTTCAAAATTGGGGGATTGAACCCATTGACAATGTCATGGGAATG
+ATAGGAATATTACCTGACATGACTCCGAGCACAGAGATGTCGCTGAGAGGGGTGAGGGTC
+AGTAAGATGGGAGTGGATGAATATTCCAGCACCGAGAGAGTGGTCGTGAGTATTGACCGT
+TTCTTAAGAGTTCGAGATCAGCGTGGAAATGTACTCCTGTCTCCTGAAGAGGTTAGCGAA
+ACGCAGGGAACAGAGAAGTTGACCATAACATATTCATCATCAATGATGTGGGAAATTAAT
+GGCCCTGAGTCAGTGCTAGTTAATACCTATCAATGGATCATCAGAAATTGGGAGACTGTG
+AAGATTCAGTGGTCCCAGGTCCCTGCAATACTATACAACAAAATGGAGTTTGAACCTTTC
+CAGTCCTTGGTACCTAAGGCTGCCAGAGGCCAATACAGTGGGTTTGTGAGAACACTGTTC
+CAACAGATGCGTGACGTTCTTGGGACATTCGACACAGTTCAGATAATAAAATTGCTTCCC
+TTTGCAGCGGCCCCACCGGAGCAGAGTAGGATGCAATTCTCTTCTCTAACTGTGAATGTA
+AGAGGGTCAGGAATGAGAATACTTGTGAGAGGTAATTCCCCTGTATTCAATTATAACAAG
+GCAACCAAGAGGCTTACAGTCCTCGGGAAGGACGCGGGTGCGTTAACAGAAGACCCAGGT
+GAAGGCACAGCTGGAGTGGAATCTGCTGTTTTGAGAGGGTTTCTAATTCTGGGCAAAGAA
+GACAAAAGATATGGACCAGCATTGAGCATCAATGAACTGAGCAATCTTGCGAAAGGGGAG
+AAAGCTAACGTGTTAATAGGGCAAGGAGACGTGGTGTTGGTAATGAAACGGAAACGGGAC
+TCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAA
+>NC_026431.1 |Influenza A virus (A/California/07/2009(H1N1)) segment 7 matrix protein 2 (M2) and matrix protein 1 (M1) genes, complete cds
+ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTTTCTATCATCCCGTCAGGCCCCCTC
+AAAGCCGAGATCGCGCAGAGACTGGAAAGTGTCTTTGCAGGAAAGAACACAGATCTTGAG
+GCTCTCATGGAATGGCTAAAGACAAGACCAATCTTGTCACCTCTGACTAAGGGAATTTTA
+GGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTC
+CAAAATGCCCTAAATGGGAATGGGGACCCGAACAACATGGATAGAGCAGTTAAACTATAC
+AAGAAGCTCAAAAGAGAAATAACGTTCCATGGGGCCAAGGAGGTGTCACTAAGCTATTCA
+ACTGGTGCACTTGCCAGTTGCATGGGCCTCATATACAACAGGATGGGAACAGTGACCACA
+GAAGCTGCTTTTGGTCTAGTGTGTGCCACTTGTGAACAGATTGCTGATTCACAGCATCGG
+TCTCACAGACAGATGGCTACTACCACCAATCCACTAATCAGGCATGAAAACAGAATGGTG
+CTGGCTAGCACTACGGCAAAGGCTATGGAACAGATGGCTGGATCGAGTGAACAGGCAGCG
+GAGGCCATGGAGGTTGCTAATCAGACTAGGCAGATGGTACATGCAATGAGAACTATTGGG
+ACTCATCCTAGCTCCAGTGCTGGTCTGAAAGATGACCTTCTTGAAAATTTGCAGGCCTAC
+CAGAAGCGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTCGTCATTGCAGCAAA
+TATCATTGGGATCTTGCACCTGATATTGTGGATTACTGATCGTCTTTTTTTCAAATGTAT
+TTATCGTCGCTTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGAGTGCCTGAGTC
+CATGAGGGAAGAATATCAACAGGAACAGCAGAGTGCTGTGGATGTTGACGATGGTCATTT
+TGTCAACATAGAGCTAGAGTAA
+>NC_026432.1 |Influenza A virus (A/California/07/2009(H1N1)) segment 8 nuclear export protein (NEP) and nonstructural protein 1 (NS1) genes, complete cds
+ATGGACTCCAACACCATGTCAAGCTTTCAGGTAGACTGTTTCCTTTGGCATATCCGCAAG
+CGATTTGCAGACAATGGATTGGGTGATGCCCCATTCCTTGATCGGCTCCGCCGAGATCAA
+AAGTCCTTAAAAGGAAGAGGCAACACCCTTGGCCTCGATATCGAAACAGCCACTCTTGTT
+GGGAAACAAATCGTGGAATGGATCTTGAAAGAGGAATCCAGCGAGACACTTAGAATGACA
+ATTGCATCTGTACCTACTTCGCGCTACCTTTCTGACATGACCCTCGAGGAAATGTCACGA
+GACTGGTTCATGCTCATGCCTAGGCAAAAGATAATAGGCCCTCTTTGCGTGCGATTGGAC
+CAGGCGATCATGGAAAAGAACATAGTACTGAAAGCGAACTTCAGTGTAATCTTTAACCGA
+TTAGAGACCTTGATACTACTAAGGGCTTTCACTGAGGAGGGAGCAATAGTTGGAGAAATT
+TCACCATTACCTTCTCTTCCAGGACATACTTATGAGGATGTCAAAAATGCAGTTGGGGTC
+CTCATCGGAGGACTTGAATGGAATGGTAACACGGTTCGAGTCTCTGAAAATATACAGAGA
+TTCGCTTGGAGAAACTGTGATGAGAATGGGAGACCTTCACTACCTCCAGAGCAGAAATGA
+AAAGTGGCGAGAGCAATTGGGACAGAAATTTGAGGAAATAAGGTGGTTAATTGAAGAAAT
+GCGGCACAGATTGAAAGCGACAGAGAATAGTTTCGAACAAATAACATTTATGCAAGCCTT
+ACAACTACTGCTTGAAGTAGAACAAGAGATAAGAGCTTTCTCGTTTCAGCTTATTTAATG
+ATAAAAAACACCCTTGTTTCTAC
+>NC_026433.1 |Influenza A virus (A/California/07/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds
+ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTA
+TGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAAT
+GTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAA
+CTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGA
+AATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCT
+AGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAG
+CAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGG
+CCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGC
+TTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAA
+TCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCT
+ACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCA
+TCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGRTCRA
+GAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAA
+GCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCT
+GGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAG
+GGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGT
+CCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCT
+ATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGG
+ATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCC
+GACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATT
+GAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGA
+ATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCC
+GAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAG
+AACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGC
+TGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACT
+TATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTA
+AAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCA
+TTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTA
+CAGTGTAGAATATGTATTTAA
+>NC_026434.1 |Influenza A virus (A/California/07/2009(H1N1)) segment 6 neuraminidase (NA) gene, complete cds
+ATGAATCCAAACCAAAAGATAATAACCATTGGTTCGGTCTGTATGACAATTGGAATGGCT
+AACTTAATATTACAAATTGGAAACATAATCTCAATATGGATTAGCCACTCAATTCAACTT
+GGGAATCAAAATCAGATTGAAACATGCAATCAAAGCGTCATTACTTATGAAAACAACACT
+TGGGTAAATCAGACATATGTTAACATCAGCAACACCAACTTTGCTGCTGGACAGTCAGTG
+GTTTCCGTGAAATTAGCGGGCAATTCCTCTCTCTGCCCTGTTAGTGGATGGGCTATATAC
+AGTAAAGACAACAGTGTAAGAATCGGTTCCAAGGGGGATGTGTTTGTCATAAGGGAACCA
+TTCATATCATGCTCCCCCTTGGAATGCAGAACCTTCTTCTTGACTCAAGGGGCCTTGCTA
+AATGACAAACATTCCAATGGAACCATTAAAGACAGGAGCCCATATCGAACCCTAATGAGC
+TGTCCTATTGGTGAAGTTCCCTCTCCATACAACTCAAGATTTGAGTCAGTCGCTTGGTCA
+GCAAGTGCTTGTCATGATGGCATCAATTGGCTAACAATTGGAATTTCTGGCCCAGACAAT
+GGGGCAGTGGCTGTGTTAAAGTACAACGGCATAATAACAGACACTATCAAGAGTTGGAGA
+AACAATATATTGAGAACACAAGAGTCTGAATGTGCATGTGTAAATGGTTCTTGCTTTACT
+GTAATGACCGATGGACCAAGTAATGGACAGGCCTCATACAAGATCTTCAGAATAGAAAAG
+GGAAAGATAGTCAAATCAGTCGAAATGAATGCCCCTAATTATCACTATGAGGAATGCTCC
+TGTTATCCTGATTCTAGTGAAATCACATGTGTGTGCAGGGATAACTGGCATGGCTCGAAT
+CGACCGTGGGTGTCTTTCAACCAGAATCTGGAATATCAGATAGGATACATATGCAGTGGG
+ATTTTCGGAGACAATCCACGCCCTAATGATAAGACAGGCAGTTGTGGTCCAGTATCGTCT
+AATGGAGCAAATGGAGTAAAAGGGTTTTCATTCAAATACGGCAATGGTGTTTGGATAGGG
+AGAACTAAAAGCATTAGTTCAAGAAACGGTTTTGAGATGATTTGGGATCCGAACGGATGG
+ACTGGGACAGACAATAACTTCTCAATAAAGCAAGATATCGTAGGAATAAATGAGTGGTCA
+GGATATAGCGGGAGTTTTGTTCAGCATCCAGAACTAACAGGGCTGGATTGTATAAGACCT
+TGCTTCTGGGTTGAACTAATCAGAGGGCGACCCAAAGAGAACACAATCTGGACTAGCGGG
+AGCAGCATATCCTTTTGTGGTGTAAACAGTGACACTGTGGGTTGGTCTTGGCCAGACGGT
+GCTGAGTTGCCATTTACCATTGACAAGTAA
+>NC_026436.1 |Influenza A virus (A/California/07/2009(H1N1)) segment 5 nucleocapsid protein (NP) gene, complete cds
+ATGGCGTCTCAAGGCACCAAACGATCATATGAACAAATGGAGACTGGTGGGGAGCGCCAG
+GATGCCACAGAAATCAGAGCATCTGTCGGAAGAATGATTGGTGGAATCGGGAGATTCTAC
+ATCCAAATGTGCACTGAACTCAAACTCAGTGATTATGATGGACGACTAATCCAGAATAGC
+ATAACAATAGAGAGGATGGTGCTTTCTGCTTTTGATGAGAGAAGAAATAAATACCTAGAA
+GAGCATCCCAGTGCTGGGAAGGACCCTAAGAAAACAGGAGGACCCATATATAGAAGAGTA
+GACGGAAAGTGGATGAGAGAACTCATCCTTTATGACAAAGRAGAAATAAGGAGAGTTTGG
+CGCCTAGCAAACAATGGCGAAGATGCAACAGCAGGTCTTACTCATATCATGATTTGGCAT
+TCCAACCTGAATGATGCCACATATCAGAGAACAAGAGCGCTTGTTCGCACCGGAATGGAT
+CCCAGAATGTGCTCTCTAATGCAAGGTTCAACACTTCCCAGAAGGTCTGGTGCCGCAGGT
+GCTGCGGTGAAAGGAGTTGGAACAATAGCAATGGAGTTAATCAGAATGATCAAACGTGGA
+ATCAATGACCGAAATTTCTGGAGGGGTGAAAATGGACGAAGGACAAGGGTTGCTTATGAA
+AGAATGTGCAATATCCTCAAAGGAAAATTTCAAACAGCTGCCCAGAGGGCAATGATGGAT
+CAAGTAAGAGAAAGTCGAAACCCAGGAAACGCTGAGATTGAAGACCTCATTTTCCTGGCA
+CGGTCAGCACTCATTCTGAGGGGATCAGTTGCACATAAATCCTGCCTGCCTGCTTGTGTG
+TATGGGCTTGCAGTAGCAAGTGGGCATGACTTTGAAAGGGAAGGGTACTCACTGGTCGGG
+ATAGACCCATTCAAATTACTCCAAAACAGCCAAGTGGTCAGCCTGATGAGACCAAATGAA
+AACCCAGCTCACAAGAGTCAATTGGTGTGGATGGCATGCCACTCTGCTGCATTTGAAGAT
+TTAAGAGTATCAAGTTTCATAAGAGGAAAGAAAGTGATTCCAAGAGGAAAGCTTTCCACA
+AGAGGGGTCCAGATTGCTTCAAATGAGAATGTGGAAACCATGGACTCCAATACCCTGGAA
+CTGAGAAGCAGATACTGGGCCATAAGGACCAGGAGTGGAGGAAATACCAATCAACAAAAG
+GCATCCGCAGGCCAGATCAGTGTGCAGCCTACATTCTCAGTGCAGCGGAATCTCCCTTTT
+GAAAGAGCAACCGTTATGGCAGCATTCAGCGGGAACAATGAAGGACGGACATCCGACATG
+CGAACAGAAGTTATAAGAATGATGGAAAGTGCAAAGCCAGAAGATTTGTCCTTCCAGGGG
+CGGGGAGTCTTCGAGCTCTCGGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGAC
+ATGAGTAATGAAGGGTCTTATTTCTTCGGAGACAATGCAGAGGAGTATGACAGTTGA

primerschemes/artic-flu-a/800/v1.0.0/work/config.json

@@ -0,0 +1,63 @@
+{
+    "amplicon_size": 800,
+    "amplicon_size_max": 880,
+    "amplicon_size_min": 720,
+    "backtrack": false,
+    "circular": false,
+    "dimer_score": -28.0,
+    "dna_conc": 15.0,
+    "dntp_conc": 0.8,
+    "dv_conc": 2.0,
+    "editdist_max": 1,
+    "force": true,
+    "high_gc": false,
+    "ignore_n": false,
+    "input_bedfile": null,
+    "mapping": "first",
+    "min_base_freq": 0.007,
+    "min_overlap": 10,
+    "mismatch_fuzzy": true,
+    "mismatch_kmersize": 19,
+    "mismatch_product_size": 0,
+    "msa_data": {
+        "0": {
+            "msa_checksum": "364e75ff18a565bf9dac9485538a3464",
+            "msa_chromname": "pa_1934_Avian_A_chicken_Germany_1934_Germany_H7N1",
+            "msa_name": "pa.x.dup.filt",
+            "msa_path": "work/pa.x.dup.filt.fasta",
+            "msa_uuid": "7eadac13"
+        },
+        "1": {
+            "msa_checksum": "30f8da0f5b5726136e1134e64cc43f1e",
+            "msa_chromname": "pb1_1934_Avian_A_chicken_Germany_1934_Germany_H7N1",
+            "msa_name": "pb1.x.dup.filt",
+            "msa_path": "work/pb1.x.dup.filt.fasta",
+            "msa_uuid": "8af2b8a2"
+        },
+        "2": {
+            "msa_checksum": "307b6beaaa46cfc2499abfc917d77988",
+            "msa_chromname": "pb2_1934_Avian_A_chicken_Rostock_45_1934_Germany_H7N1",
+            "msa_name": "pb2.x.dup.filt",
+            "msa_path": "work/pb2.x.dup.filt.fasta",
+            "msa_uuid": "ee945c1d"
+        }
+    },
+    "mv_conc": 100.0,
+    "n_pools": 2,
+    "ncores": 8,
+    "output": "/Users/kentcg/schemes/artic-flu/v2/schemes/first-tuni-hack-filt-0.007",
+    "primer_annealing_prop": null,
+    "primer_annealing_tempc": 65,
+    "primer_gc_max": 55,
+    "primer_gc_min": 30,
+    "primer_hairpin_th_max": 47.0,
+    "primer_homopolymer_max": 5,
+    "primer_max_walk": 80,
+    "primer_size_max": 34,
+    "primer_size_min": 19,
+    "primer_tm_max": 62.5,
+    "primer_tm_min": 59.5,
+    "use_annealing": false,
+    "use_matchdb": true,
+    "version": "3.2.0"
+}