Merge pull request #25 from ChrisgKent/main

Added schemes and updated status
quick-lab · Mar 14, 2024 · b4d20f6 · b4d20f6
2 parents 61152ce + b8ea92b
commit b4d20f6
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Showing 21 changed files with 291,176 additions and 32 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1 +1,2 @@
-
+**.fai
+.DS_Store
diff --git a/index.json b/index.json
@@ -1,5 +1,5 @@
 {
-    "github-commit-sha": "37262064a37de3ca1a5498088ba154119d2ecd90",
+    "github-commit-sha": "124367a0243d03d5b3bb57dd9e8c328f9e6759c7",
     "primerschemes": {
         "artic-measles": {
             "400": {
@@ -13,10 +13,10 @@
                     ],
                     "citations": [],
                     "collections": [
-                        "WHOLE-GENOME",
-                        "ARTIC",
                         "WASTE-WATER",
-                        "QUICK-LAB"
+                        "QUICK-LAB",
+                        "WHOLE-GENOME",
+                        "ARTIC"
                     ],
                     "info_json_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/artic-measles/400/v1.0.0/info.json",
                     "license": "CC BY-SA 4.0",
@@ -30,7 +30,7 @@
                     "species": [
                         11234
                     ],
-                    "status": "draft"
+                    "status": "tested"
                 }
             }
         },
@@ -375,14 +375,14 @@
                     "ampliconsize": 600,
                     "articbedversion": "v3.0",
                     "authors": [
-                        "Quick Lab",
                         "Dr Sheila Lumley",
-                        "Chris Kent"
+                        "Chris Kent",
+                        "Quick Lab"
                     ],
                     "citations": [],
                     "collections": [
-                        "QUICK-LAB",
-                        "WHOLE-GENOME"
+                        "WHOLE-GENOME",
+                        "QUICK-LAB"
                     ],
                     "info_json_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/hbv/600/v2.0.0/info.json",
                     "license": "CC BY-SA 4.0",
@@ -397,6 +397,34 @@
                         10407
                     ],
                     "status": "tested"
+                },
+                "v2.1.0": {
+                    "algorithmversion": "primalscheme3:1.1.4",
+                    "ampliconsize": 600,
+                    "articbedversion": "v3.0",
+                    "authors": [
+                        "Chris Kent c.g.kent@bham.ac.uk",
+                        "Dr Sheila Lumley sheila.lumley@trinity.ox.ac.uk",
+                        "Quick Lab"
+                    ],
+                    "citations": [],
+                    "collections": [
+                        "QUICK-LAB",
+                        "WHOLE-GENOME"
+                    ],
+                    "info_json_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes-fork/main/primerschemes/hbv/600/v2.1.0/info.json",
+                    "license": "CC BY-SA 4.0",
+                    "primer_bed_md5": "5af354939e06acc830f7f340720a94b1",
+                    "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes-fork/main/primerschemes/hbv/600/v2.1.0/primer.bed",
+                    "primerclass": "primerschemes",
+                    "reference_fasta_md5": "b0c81b63db38a860016236b68977f38e",
+                    "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes-fork/main/primerschemes/hbv/600/v2.1.0/reference.fasta",
+                    "schemename": "hbv",
+                    "schemeversion": "v2.1.0",
+                    "species": [
+                        10407
+                    ],
+                    "status": "draft"
                 }
             }
         },
@@ -490,7 +518,7 @@
                     "species": [
                         122929
                     ],
-                    "status": "draft"
+                    "status": "tested"
                 }
             }
         },

diff --git a/primerschemes/artic-measles/400/v1.0.0/README.md b/primerschemes/artic-measles/400/v1.0.0/README.md
@@ -17,7 +17,7 @@ A pan Measles morbillivirus scheme. All full length genomes have been downloaded
     "schemename": "artic-measles",
     "primer_bed_md5": "b8b903356d4c6bd4dc03af04f3a18222",
     "reference_fasta_md5": "2c3dd74742a333dffb50bcfbd158bfbd",
-    "status": "draft",
+    "status": "tested",
     "citations": [],
     "authors": [
         "Chris Kent",
@@ -34,10 +34,10 @@ A pan Measles morbillivirus scheme. All full length genomes have been downloaded
     "description": "A pan Measles morbillivirus scheme. All full length genomes have been downloaded and phylogenicly downsampled to 0.95 RTL.",
     "derivedfrom": null,
     "collections": [
-        "WHOLE-GENOME",
-        "ARTIC",
         "WASTE-WATER",
-        "QUICK-LAB"
+        "QUICK-LAB",
+        "WHOLE-GENOME",
+        "ARTIC"
     ]
 }
 ```

diff --git a/primerschemes/artic-measles/400/v1.0.0/info.json b/primerschemes/artic-measles/400/v1.0.0/info.json
@@ -4,7 +4,7 @@
     "schemename": "artic-measles",
     "primer_bed_md5": "b8b903356d4c6bd4dc03af04f3a18222",
     "reference_fasta_md5": "2c3dd74742a333dffb50bcfbd158bfbd",
-    "status": "draft",
+    "status": "tested",
     "citations": [],
     "authors": [
         "Chris Kent",
@@ -21,9 +21,9 @@
     "description": "A pan Measles morbillivirus scheme. All full length genomes have been downloaded and phylogenicly downsampled to 0.95 RTL.",
     "derivedfrom": null,
     "collections": [
-        "WHOLE-GENOME",
-        "ARTIC",
         "WASTE-WATER",
-        "QUICK-LAB"
+        "QUICK-LAB",
+        "WHOLE-GENOME",
+        "ARTIC"
     ]
 }
diff --git a/primerschemes/hbv/600/v2.0.0/README.md b/primerschemes/hbv/600/v2.0.0/README.md
@@ -2,7 +2,7 @@
 
 ## Description
 
-A 800bp high overlap scheme for HBV. Using phylogenetic downsampling to reduce bias in under represented HBV Clades
+A 600bp high overlap scheme for HBV. Using phylogenetic downsampling to reduce bias in under represented HBV Clades
 
 ## Overviews
 
@@ -20,9 +20,9 @@ A 800bp high overlap scheme for HBV. Using phylogenetic downsampling to reduce b
     "status": "tested",
     "citations": [],
     "authors": [
-        "Quick Lab",
         "Dr Sheila Lumley",
-        "Chris Kent"
+        "Chris Kent",
+        "Quick Lab"
     ],
     "algorithmversion": "primalscheme3:1.1.3",
     "species": [
@@ -32,11 +32,11 @@ A 800bp high overlap scheme for HBV. Using phylogenetic downsampling to reduce b
     "primerclass": "primerschemes",
     "infoschema": "v1.3.0",
     "articbedversion": "v3.0",
-    "description": "A 800bp high overlap scheme for HBV. Using phylogenetic downsampling to reduce bias in under represented HBV Clades",
+    "description": "A 600bp high overlap scheme for HBV. Using phylogenetic downsampling to reduce bias in under represented HBV Clades",
     "derivedfrom": null,
     "collections": [
-        "QUICK-LAB",
-        "WHOLE-GENOME"
+        "WHOLE-GENOME",
+        "QUICK-LAB"
     ]
 }
 ```

diff --git a/primerschemes/hbv/600/v2.0.0/info.json b/primerschemes/hbv/600/v2.0.0/info.json
@@ -7,9 +7,9 @@
     "status": "tested",
     "citations": [],
     "authors": [
-        "Quick Lab",
         "Dr Sheila Lumley",
-        "Chris Kent"
+        "Chris Kent",
+        "Quick Lab"
     ],
     "algorithmversion": "primalscheme3:1.1.3",
     "species": [
@@ -19,10 +19,10 @@
     "primerclass": "primerschemes",
     "infoschema": "v1.3.0",
     "articbedversion": "v3.0",
-    "description": "A 800bp high overlap scheme for HBV. Using phylogenetic downsampling to reduce bias in under represented HBV Clades",
+    "description": "A 600bp high overlap scheme for HBV. Using phylogenetic downsampling to reduce bias in under represented HBV Clades",
     "derivedfrom": null,
     "collections": [
-        "QUICK-LAB",
-        "WHOLE-GENOME"
+        "WHOLE-GENOME",
+        "QUICK-LAB"
     ]
 }
diff --git a/primerschemes/hbv/600/v2.1.0/README.md b/primerschemes/hbv/600/v2.1.0/README.md
@@ -0,0 +1,50 @@
+# hbv 600bp v2.1.0
+
+## Description
+
+Contains additional Spike in primers for clades G and H
+
+## Overviews
+
+![X02763.png](work/X02763.png)
+
+## Details
+
+```json
+{
+    "ampliconsize": 600,
+    "schemeversion": "v2.1.0",
+    "schemename": "hbv",
+    "primer_bed_md5": "5af354939e06acc830f7f340720a94b1",
+    "reference_fasta_md5": "b0c81b63db38a860016236b68977f38e",
+    "status": "draft",
+    "citations": [],
+    "authors": [
+        "Chris Kent c.g.kent@bham.ac.uk",
+        "Dr Sheila Lumley sheila.lumley@trinity.ox.ac.uk",
+        "Quick Lab"
+    ],
+    "algorithmversion": "primalscheme3:1.1.4",
+    "species": [
+        10407
+    ],
+    "license": "CC BY-SA 4.0",
+    "primerclass": "primerschemes",
+    "infoschema": "v1.3.0",
+    "articbedversion": "v3.0",
+    "description": "Contains additional Spike in primers for clades G and H",
+    "derivedfrom": "hbv/600/v2.0.0",
+    "collections": [
+        "QUICK-LAB",
+        "WHOLE-GENOME"
+    ]
+}
+```
+
+
+
+------------------------------------------------------------------------
+
+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)
diff --git a/primerschemes/hbv/600/v2.1.0/info.json b/primerschemes/hbv/600/v2.1.0/info.json
@@ -0,0 +1,28 @@
+{
+    "ampliconsize": 600,
+    "schemeversion": "v2.1.0",
+    "schemename": "hbv",
+    "primer_bed_md5": "5af354939e06acc830f7f340720a94b1",
+    "reference_fasta_md5": "b0c81b63db38a860016236b68977f38e",
+    "status": "draft",
+    "citations": [],
+    "authors": [
+        "Chris Kent c.g.kent@bham.ac.uk",
+        "Dr Sheila Lumley sheila.lumley@trinity.ox.ac.uk",
+        "Quick Lab"
+    ],
+    "algorithmversion": "primalscheme3:1.1.4",
+    "species": [
+        10407
+    ],
+    "license": "CC BY-SA 4.0",
+    "primerclass": "primerschemes",
+    "infoschema": "v1.3.0",
+    "articbedversion": "v3.0",
+    "description": "Contains additional Spike in primers for clades G and H",
+    "derivedfrom": "hbv/600/v2.0.0",
+    "collections": [
+        "QUICK-LAB",
+        "WHOLE-GENOME"
+    ]
+}