Merge pull request #22 from ChrisgKent/main

Added scheme. Changed status

primerschemes/artic-measles/400/v1.0.0/README.md

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+# artic-measles 400bp v1.0.0
+
+## Description
+
+A pan Measles morbillivirus scheme. All full length genomes have been downloaded and phylogenicly downsampled to 0.95 RTL.
+
+## Overviews
+
+![NC_001498.1.png](work/NC_001498.1.png)
+
+## Details
+
+```json
+{
+    "ampliconsize": 400,
+    "schemeversion": "v1.0.0",
+    "schemename": "artic-measles",
+    "primer_bed_md5": "b8b903356d4c6bd4dc03af04f3a18222",
+    "reference_fasta_md5": "2c3dd74742a333dffb50bcfbd158bfbd",
+    "status": "draft",
+    "citations": [],
+    "authors": [
+        "Chris Kent",
+        "Quick Lab"
+    ],
+    "algorithmversion": "primalscheme3:1.1.4",
+    "species": [
+        11234
+    ],
+    "license": "CC BY-SA 4.0",
+    "primerclass": "primerschemes",
+    "infoschema": "v1.2.0",
+    "articbedversion": "v3.0",
+    "description": "A pan Measles morbillivirus scheme. All full length genomes have been downloaded and phylogenicly downsampled to 0.95 RTL.",
+    "derivedfrom": 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-measles/400/v1.0.0/info.json

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+{
+    "ampliconsize": 400,
+    "schemeversion": "v1.0.0",
+    "schemename": "artic-measles",
+    "primer_bed_md5": "b8b903356d4c6bd4dc03af04f3a18222",
+    "reference_fasta_md5": "2c3dd74742a333dffb50bcfbd158bfbd",
+    "status": "draft",
+    "citations": [],
+    "authors": [
+        "Chris Kent",
+        "Quick Lab"
+    ],
+    "algorithmversion": "primalscheme3:1.1.4",
+    "species": [
+        11234
+    ],
+    "license": "CC BY-SA 4.0",
+    "primerclass": "primerschemes",
+    "infoschema": "v1.2.0",
+    "articbedversion": "v3.0",
+    "description": "A pan Measles morbillivirus scheme. All full length genomes have been downloaded and phylogenicly downsampled to 0.95 RTL.",
+    "derivedfrom": null
+}

primerschemes/artic-measles/400/v1.0.0/work/amplicon.bed

@@ -0,0 +1,47 @@
+NC_001498.1	1	437	177e6ebb_0	1
+NC_001498.1	359	827	177e6ebb_1	2
+NC_001498.1	744	1217	177e6ebb_2	1
+NC_001498.1	1103	1548	177e6ebb_3	2
+NC_001498.1	1404	1834	177e6ebb_4	1
+NC_001498.1	1739	2200	177e6ebb_5	2
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+NC_001498.1	2419	2888	177e6ebb_7	2
+NC_001498.1	2770	3205	177e6ebb_8	1
+NC_001498.1	3140	3608	177e6ebb_9	2
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+NC_001498.1	11941	12376	177e6ebb_35	2
+NC_001498.1	12298	12747	177e6ebb_36	1
+NC_001498.1	12550	12977	177e6ebb_37	2
+NC_001498.1	12875	13341	177e6ebb_38	1
+NC_001498.1	13257	13705	177e6ebb_39	2
+NC_001498.1	13584	14037	177e6ebb_40	1
+NC_001498.1	13901	14305	177e6ebb_41	2
+NC_001498.1	14216	14684	177e6ebb_42	1
+NC_001498.1	14556	15010	177e6ebb_43	2
+NC_001498.1	14900	15343	177e6ebb_44	1
+NC_001498.1	15224	15671	177e6ebb_45	2
+NC_001498.1	15429	15889	177e6ebb_46	1

primerschemes/artic-measles/400/v1.0.0/work/config.json

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+{
+    "algorithmversion": "primalscheme3:1.1.4",
+    "amplicon_size_max": 440,
+    "amplicon_size_min": 360,
+    "backtrack": true,
+    "bedfile": false,
+    "circular": false,
+    "dimerscore": -26,
+    "disable_progress_bar": false,
+    "dna_conc": 15.0,
+    "dntp_conc": 0.8,
+    "dv_conc": 2.0,
+    "editdist_end3p": 6,
+    "editdist_max": 1,
+    "force": true,
+    "mapping": "first",
+    "min_overlap": 20,
+    "minbasefreq": 0.01,
+    "mismatch_fuzzy": true,
+    "mismatch_kmersize": 18,
+    "mismatch_product_size": 440,
+    "msa_data": {
+        "0": {
+            "msa_checksum": "7aa97c18e478e865a8a026b876c8753c",
+            "msa_chromname": "NC_001498.1",
+            "msa_name": "all_genomes.align.ds.align.repaired",
+            "msa_path": "work/all_genomes.align.ds.align.repaired.fasta",
+            "msa_uuid": "177e6ebb"
+        }
+    },
+    "mv_conc": 100.0,
+    "n_cores": 8,
+    "npools": 2,
+    "plot": true,
+    "primer_gc_max": 67.0,
+    "primer_gc_min": 30,
+    "primer_hairpin_th_max": 47.0,
+    "primer_homopolymer_max": 5,
+    "primer_max_walk": 80,
+    "primer_size_max": 36,
+    "primer_size_min": 18,
+    "primer_tm_max": 62.5,
+    "primer_tm_min": 59.5,
+    "primerclass": "primerschemes",
+    "reducekmers": false
+}