Merge pull request #111 from nextstrain/update-rsv

rsv: update datasets with new consortium nomenclature

data/nextstrain/rsv/a/EPI_ISL_412866/CHANGELOG.md

@@ -1,7 +1,5 @@
 ## Unreleased
 
-Initial release for Nextclade v3!
+**first release of v3 dataset.**
 
-This dataset is converted from the corresponding older dataset for Nextclade v2. You can find old versions of datasets here: https://github.com/nextstrain/nextclade_data/tree/2023-08-17--15-51-24--UTC/data/datasets
-
-Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
+Updated consortium nomenclature.

data/nextstrain/rsv/a/EPI_ISL_412866/README.md

@@ -1,14 +1,20 @@
-# Nextclade dataset for "RSV-A" based on reference "hRSV/A/England/397/2017" (rsv_a/EPI_ISL_412866)
+# RSV-A dataset with reference genome A/England/397/2017
 
+| Key                    | Value                                                                                                               |
+| ---------------------- | --------------------------------------------------------------------------------------------------------------------|
+| authors                | [Richard Neher](https://neherlab.org), Laura Urbanska, [Nextstrain](https://nextstrain.org)                         |
+| data source            | Genbank + authorized other sequences                                                                                |
+| workflow               | [github.com/nextstrain/rsv/nextclade](https://github.com/nextstrain/rsv/nextclade)                                  |
+| nextclade dataset path | nextstrain/rsv/a/EPI_ISL_412866                                                                                     |
+| reference              | EPI_ISL_412866                                                                                                      |
+| clade definitions      | [github.com/rsv-lineages/lineage-designation-A](https://github.com/rsv-lineages/lineage-designation-A)              |
 
-## Dataset attributes
+## Scope of this dataset
+This dataset for RSV-B uses reference sequence A/England/397/2017 with is available at under accession number EPI_ISL_412866 in GISAID. An almost identical sequence (slightly longer, 12 mutations, no gaps or indels) is available in NCBI as [LR699737](https://www.ncbi.nlm.nih.gov/nuccore/LR699737).
+This sequence has the duplication in the G-protein shared by all currently circulating variants.
+The reference tree covers the diversity of RSV-A since the first sequenced samples.
 
-| attribute            | value                | value friendly                           |
-| -------------------- | -------------------- | ---------------------------------------- |
-| name                 | rsv_a                | RSV-A                                    |
-| reference            | EPI_ISL_412866       | hRSV/A/England/397/2017                  |
 
-
-## What is Nextclade dataset
-
-Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
+## Nomenclature
+The dataset follows the consortium nomenclature established in 2023 that uses a combination of letters and numbers to designate lineages in a hierarchical fashion.
+Definitions of individuals lineages are available on github in the repository [rsv-lineages/lineage-designation-A](https://github.com/rsv-lineages/lineage-designation-A).

data/nextstrain/rsv/a/EPI_ISL_412866/genome_annotation.gff3

@@ -1,14 +1,16 @@
 ##gff-version 3
 ##sequence-region EPI_ISL_412866 1 15225
-EPI_ISL_412866	feature	source	1	15225	.	.	.	mol_type=viral cRNA;organism=Human respiratory syncytial virus A
-EPI_ISL_412866	feature	gene	70	489	.	.	0	codon_start=1;gene_name=NS1;product=nonstructural protein 1;protein_id=VVF34488.1
-EPI_ISL_412866	feature	gene	599	973	.	.	0	codon_start=1;gene_name=NS2;product=nonstructural protein 2;protein_id=VVF34491.1
-EPI_ISL_412866	feature	gene	1111	2286	.	.	0	codon_start=1;gene_name=N;product=nucleoprotein;protein_id=VVF34494.1
-EPI_ISL_412866	feature	gene	2318	3043	.	.	0	codon_start=1;gene_name=P;product=phosphoprotein;protein_id=VVF34497.1
-EPI_ISL_412866	feature	gene	3226	3996	.	.	0	codon_start=1;gene_name=M;product=matrix protein;protein_id=VVF34500.1
-EPI_ISL_412866	feature	gene	4266	4460	.	.	0	codon_start=1;gene_name=SH;product=small hydrophobic protein;protein_id=VVF34503.1
-EPI_ISL_412866	feature	gene	4652	5617	.	.	0	codon_start=1;gene_name=G;product=attachment glycoprotein;protein_id=VVF34506.1
-EPI_ISL_412866	feature	gene	5697	7421	.	.	0	codon_start=1;gene_name=F;product=fusion glycoprotein;protein_id=VVF34509.1
-EPI_ISL_412866	feature	gene	7640	8224	.	.	0	codon_start=1;gene_name=M2-1;product=M2-1 protein;protein_id=VVF34512.1
-EPI_ISL_412866	feature	gene	8193	8465	.	.	0	codon_start=1;gene_name=M2-2;product=M2-2 protein;protein_id=VVF34515.1
-EPI_ISL_412866	feature	gene	8523	15029	.	.	0	codon_start=1;gene_name=L;product=polymerase protein;protein_id=VVF34518.1
+EPI_ISL_412866	annotation	remark	1	15225	.	.	.	molecule_type=cRNA;organism=Human orthopneumovirus;taxonomy=Viruses,Riboviria,Orthornavirae,Negarnaviricota,Haploviricotina,Monjiviricetes,Mononegavirales,Pneumoviridae,Orthopneumovirus,Orthopneumovirus hominis
+EPI_ISL_412866	feature	source	1	15225	.	.	.	mol_type=viral cRNA;organism=Human orthopneumovirus
+EPI_ISL_412866	feature	5'UTR	1	15	.	.	.	citation=%5B1%5D;function=Leader region 5%27UTR
+EPI_ISL_412866	feature	CDS	70	489	.	.	0	codon_start=1;db_xref=GeneID:37607636;gene=NS1;gene_name=NS1;Name=NS1;product=nonstructural protein 1;protein_id=YP_009518850.1;translation=MGSNSLSMIKVRLQNLFDNDEVALLKITCYTDKLIQLTNALAKAVIHTIKLNGIVFVHVITSSDICPNNNIVVKSNFTTMPVLQNGGYIWEMMELTHCSQPNGLIDDNCEIKFSKKLSDSTMTNYMNQLSELLGFDLNP%2A
+EPI_ISL_412866	feature	CDS	599	973	.	.	0	codon_start=1;db_xref=GeneID:37607637;gene=NS2;gene_name=NS2;Name=NS2;product=nonstructural protein 2;protein_id=YP_009518851.1;translation=MDTTHNDTTPQRLMITDMRPLSLETIITSLTRDIITHKFIYLINHECIVRKLDERQATFTFLVNYEMKLLHKVGSTKYKKYTEYNTKYGTFPMPIFINHDGFLECIGIKPTKHTPIIYKYDLNP%2A
+EPI_ISL_412866	feature	CDS	1111	2286	.	.	0	codon_start=1;db_xref=GeneID:37607638;gene=N;gene_name=N;Name=N;product=nucleoprotein;protein_id=YP_009518852.1;translation=MALSKVKLNDTLNKDQLLSSSKYTIQRSTGDSIDTPNYDVQKHINKLCGMLLITEDANHKFTGLIGMLYAMSRLGREDTIKILKDAGYHVKANGVDVTTHRQDINGKEMKFEVLTLASLTTEIQINIEIESRKSYKKMLKEMGEVAPEYRHDSPDCGMIILCIAALVITKLAAGDRSGLTAVIRRANNVLKNEMKRYKGLLPKDIANSFYEVFEKYPHFIDVFVHFGIAQSSTRGGSRVEGIFAGLFMNAYGAGQVMLRWGVLAKSVKNIMLGHASVQAEMEQVVEVYEYAQKLGGEAGFYHILNNPKASLLSLTQFPHFSSVVLGNAAGLGIMGEYRGTPRNQDLYDAAKVYAEQLKENGVINYSVLDLTAEELEAIKHQLNPKDNDVEL%2A
+EPI_ISL_412866	feature	CDS	2318	3043	.	.	0	codon_start=1;db_xref=GeneID:37607639;gene=P;gene_name=P;Name=P;product=phosphoprotein;protein_id=YP_009518853.1;translation=MEKFAPEFHGEDANNRATKFLESIKGKFTSPKDPKKKDSIISVNSIDIEVTKESLITSNSTIINPINETDDTVGNKPNYQRKPLVSFKEDPTPSDNPFSKLYKETIETFDNNEEESSYSYEEINDQTNDNITARLDRIDEKLSEILGMLHTLVVASAGPTSARDGIRDAMVGLREEMIEKIRTEALMTNDRLEAMARLRNEESEKMAKDTSDEVSLNPTSEKLNNLLEGNDSDNDLSLEDF%2A
+EPI_ISL_412866	feature	CDS	3226	3996	.	.	0	codon_start=1;db_xref=GeneID:37607640;gene=M;gene_name=M;Name=M;product=matrix protein;protein_id=YP_009518854.1;translation=METYVNKLHEGSTYTAAVQYNVLEKDDDPASLTIWVPMFQSSMPADLLIKELANVNILVKQISTPKGPSLRVMINSRSAVLAQMPSKFTICANVSLDERSKLAYDVTTPCEIKACSLTCLKSKNMLTTVKDLTMKTLNPTHDIIALCEFENIVTSKKVIIPTYLRSISVRNKDLNTLENITTTEFKNAITNAKIIPYSGLLLVITVTDNKGAFKYIKPQSQFIVDLGAYLEKESIYYVTTNWKHTATRFAIKPMED%2A
+EPI_ISL_412866	feature	CDS	4266	4460	.	.	0	codon_start=1;db_xref=GeneID:37607641;gene=SH;gene_name=SH;Name=SH;product=small hydrophobic protein;protein_id=YP_009518855.1;translation=MENTSITIEFSSKFWPYFTLIHMITTIISLIIIISIMIAILNKLCEYNVFHNKTFELPRARVNT%2A
+EPI_ISL_412866	feature	CDS	4652	5617	.	.	0	codon_start=1;db_xref=GeneID:37607642;gene=G;gene_name=G;Name=G;product=attachment glycoprotein;protein_id=YP_009518856.1;translation=MSKTKDQRTAKTLERTWDTLNHLLFISSCLYKLNLKSIAQITLSILAMIISTSLIIAAIIFIASANHKVTPTTAIIQDATNQIKNTTPTHLTQNPQLGISLSNLSGTTSQSTTILASTTPSAESTPQSTTVKIINTTTTQILPSKPTTKQRQNKPQNKPNNDFHFEVFNFVPCSICSNNPTCWAICKRIPNKKPGKKTTTKPTKKPTLKTTKKDPKPQTTKPKGVLTTKPTGKPTINTTKTNSRTTLLTSNTKGNPEHTSQKETIHSTTSEGYPSPSQVYTTSDQEETLHSTTSEGYPSPSQVYTTSEYLSQSLSSSNTTK%2A
+EPI_ISL_412866	feature	CDS	5697	7421	.	.	0	codon_start=1;db_xref=GeneID:37607643;gene=F;gene_name=F;Name=F;product=fusion glycoprotein;protein_id=YP_009518857.1;translation=MELPILKTNAITTILAAVTLCFASSQNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPAANSRARRELPRFMNYTLNNTKNTNVTLSKKRKRRFLGFLLGVGSAIASGIAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSSNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNIDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLHNVNAGKSTTNIMITTIIIVIIVILLALIAVGLLLYCKARSTPVTLSKDQLSGINNIAFSN%2A
+EPI_ISL_412866	feature	CDS	7640	8224	.	.	0	codon_start=1;db_xref=GeneID:37607644;gene=M2;gene_name=M2-1;Name=M2-1;note=ORF 1%2C matrix protein 2;product=M2-1 protein;protein_id=YP_009518858.1;translation=MSRRNPCKFEIRGHCLNGKRCHFSHNYFEWPPHALLVRQNFMLNRILKSMDKSIDTLSEISGAAELDRTEEYALGVVGVLESYIGSINNITKQSACVAMSKLLTELNSDDIKKLRDNEEPNSPKVRVYNTVISYIESNRKNNKQTIHLLKRLPADVLKKTIKNTLDIHKSITINNSKESTVSDTNDHAKNNDTT%2A
+EPI_ISL_412866	feature	CDS	8193	8465	.	.	0	codon_start=1;db_xref=GeneID:37607644;gene=M2;gene_name=M2-2;Name=M2-2;note=ORF 2%2C RNA processivity factor;product=M2-2 protein;protein_id=YP_009518859.1;translation=TTMPKIMILPDKYPCSINSILITSNYRVTMYNQKNTLYINQNNQNSHIYPPDQPFNEIHWTSQDLIDATQNFLQHLGITDDIYTIYILVS%2A
+EPI_ISL_412866	feature	CDS	8532	15029	.	.	0	codon_start=1;db_xref=GeneID:37607645;gene=L;gene_name=L;Name=L;note=RNA dependant RNA polymerase%3B RdRp;product=polymerase protein;protein_id=YP_009518860.1;translation=MDPIISGNSANVYLTDSYLKGVISFSECNALGSYIFNGPYLKNDYTNLISRQNPLIEHINLKKLNITQSLISKYHKGEIKIEEPTYFQSLLMTYKSMTSSEQTTTTNLLKKIIRRAIEISDVKVYAILNKLGLKEKDKIKSNNGQDEDNSVITTIIKDDILLAVKDNQSHPKADKNQSTKQKDTIKTTLLKKLMCSMQHPPSWLIHWFNLYTKLNSILTQYRSSEVKNHGFILIDNHTLSGFQFILNQYGCIVYHRELKRITVTTYNQFLTWKDISLSRLNVCLITWISNCLNTLNKSLGLRCGFNNVILTQLFLYGDCILKLFHNEGFYIIKEVEGFIMSLILNITEEDQFRKRFYNSMLNNITDAANKAQKNLLSRVCHTLLDKTISDNIINGRWIILLSKFLKLIKLAGDNNLNNLSELYFLFRIFGHPMVDERQAMDAVKVNCNETKFYLLSSLSMLRGAFIYRIIKGFVNNYNRWPTLRNAIVLPLRWLTYYKLNTYPSLLELTERDLIVLSGLRFYREFRLPKKVDLEMIINDKAISPPKNLIWTSFPRNYMPSHIQNYIEHEKLKFSDSDKSRRVLEYYLRDNKFNECDLYNCVVNQSYLNNPNHVVSLTGKERELSVGRMFAMQPGMFRQVQILAEKMIAENILQFFPESLTRYGDLELQKILELKAGISNKSNRYNDNYNNYISKCSIITDLSKFNQAFRYETSCICSDVLDELHGVQSLFSWLHLTIPHVTIICTYRHAPPYIKDHIVDLNNVDEQSGLYRYHMGGIEGWCQKLWTIEAISLLDLISLKGKFSITALINGDNQSIDISKPVRLMEGQTHAQADYLLALNSLKLLYKEYAGIGHKLKGTETYISRDMQFMSKTIQHNGVYYPASIKKVLRVGPWINTILDDFKVSLESIGSLTQELEYRGESLLCSLIFRNVWLYNQIALQLKNHALCNNKLYLDILKVLKHLKTFFNLDNIDTALTLYMNLPMLFGGGDPNLLYRSFYRRTPDFLTEAIVHSVFILSYYTNHDLKDKLQDLSDDRLNKFLTCIITFDKNPNAEFVTLMRDPQALGSERQAKITSEINRLAVTEVLSTAPNKIFSKSAQHYTTTEIDLNDIMQNIEPTYPHGLRVVYESLPFYKAEKIVNLISGTKSITNILEKTSAIDLTDIDRATEMMRKNITLLIRILPLDCNRDKREILSMENLSITELSKYVRERSWSLSNIVGVTSPSIMYTMDIKYTTSTIASGIIIEKYNVNSLTRGERGPTKPWVGSSTQEKKTMPVYNRQVLTKKQRDQIDLLAKLDWVYASIDNKDEFMEELSIGTLGLTYEKAKKLFPQYLSVNYLHRLTVSSRPCEFPASIPAYRTTNYHFDTSPINRILTEKYGDEDIDIVFQNCISFGLSLMSVVEQFTNVCPNRIILIPKLNEIHLMKPPIFTGDVDIHKLKLVIQKQHMFLPDKISLTQYVELFLSNKTLKSGSNVNSNLILAHKISDYFHNTYILSTNLAGHWILIIQLMKDSKGIFEKDWGEGYITDHMFINLKVFFNAYKTYLLCFHKGYGRAKLECDMNTSDLLCVLELIDSSYWKSMSKVFLEQKVIKYILSQDASLHRVKGCHSFKLWFLKRLNVAEFTVCPWVVNIDYHPTHMKAILTYIDLVRMGLINIDRIYIKNKHKFNDEFYTSNLFYINYNFSDNTHLLTKHIRIANSELESNYNKLYHPTPETLENILTNPVKNNEKKTLSGYCIGKNVDSIMLPSLSNKKLIKSSTMIRTNYSRQDLYNLFPTVVIDKIIDHSGNTAKSNQLYTTTSHQISLVHNSTSLYCMLPWHHINRFNFVFSSTGCKISIEYILKDLKIKDPNCIAFIGEGAGNLLLRTVVELHPDIRYIYRSLKDCNDHSLPIEFLRLYNGHINIDYGENLTIPATDATNNIHWSYLHIKFAEPISLFVCDAELPVTVNWSKIIIEWSKHVRKCKYCSSVNKCTLIVKYHAQDDIDFKLDNITILKTYVCLGSKLKGSEVYLVLTIGPANVFPVFNVVQNAKLILSRTKNFIMPKKADKESIDANIKSLIPFLCYPITKKGINTALSKLKSVVSGDILSYSIAGRNEVFSNKLINHKHMNILKWFNHVLNFRSTELNYNHLYMVESTYPHLSELLNSLTTNELKKLIKITGSLLYNFYNE%2A

data/nextstrain/rsv/a/EPI_ISL_412866/pathogen.json

@@ -1,13 +1,11 @@
 {
+  "schemaVersion": "3.0.0",
   "alignmentParams": {
-    "excessBandwidth": 30,
+    "excessBandwidth": 9,
     "terminalBandwidth": 100,
     "allowedMismatches": 4,
-    "windowSize": 15,
-    "minMatchLength": 30,
-    "minSeedCover": 0.05,
     "gapAlignmentSide": "left",
-    "kmerDistance": 10
+    "minSeedCover": 0.1
   },
   "compatibility": {
     "cli": "3.0.0-alpha.0",
@@ -23,73 +21,70 @@
     "reference": "reference.fasta",
     "treeJson": "tree.json"
   },
-  "geneOrderPreference": [
-    "F",
-    "G",
-    "L"
-  ],
   "qc": {
-    "frameShifts": {
-      "enabled": true
+    "privateMutations": {
+      "enabled": true,
+      "typical": 50,
+      "cutoff": 150,
+      "weightLabeledSubstitutions": 2,
+      "weightReversionSubstitutions": 1,
+      "weightUnlabeledSubstitutions": 1
     },
     "missingData": {
       "enabled": false,
       "missingDataThreshold": 2000,
       "scoreBias": 500
     },
+    "snpClusters": {
+      "enabled": false,
+      "windowSize": 100,
+      "clusterCutOff": 10,
+      "scoreWeight": 50
+    },
     "mixedSites": {
       "enabled": true,
       "mixedSitesThreshold": 8
     },
-    "privateMutations": {
-      "cutoff": 150,
-      "enabled": true,
-      "typical": 50,
-      "weightLabeledSubstitutions": 2,
-      "weightReversionSubstitutions": 1,
-      "weightUnlabeledSubstitutions": 1
-    },
-    "snpClusters": {
-      "clusterCutOff": 10,
-      "enabled": false,
-      "scoreWeight": 50,
-      "windowSize": 100
+    "frameShifts": {
+      "enabled": true
     },
     "stopCodons": {
-      "enabled": true
+      "enabled": true,
+      "ignoredStopCodons": []
     }
   },
-  "schemaVersion": "3.0.0",
-  "version": {
-    "tag": "unreleased"
-  },
-  "attributes": {
-    "name": "Respiratory Syncytial Virus A",
-    "reference name": "hRSV/A/England/397/2017",
-    "reference accession": "EPI_ISL_412866"
-  },
+  "geneOrderPreference": [
+    "F",
+    "G",
+    "L"
+  ],
   "maintenance": {
     "website": [
       "https://nextstrain.org",
       "https://clades.nextstrain.org"
     ],
     "documentation": [
-      "https://github.com/nextstrain/nextclade_data",
-      "https://docs.nextstrain.org/projects/nextclade"
+      "https://github.com/nextstrain/rsv"
     ],
     "source code": [
-      "https://github.com/nextstrain/nextclade_data",
-      "https://github.com/neherlab/nextclade_data_workflows"
+      "https://github.com/nextstrain/rsv"
     ],
     "issues": [
-      "https://github.com/nextstrain/nextclade_data",
-      "https://github.com/nextstrain/nextclade_data/issues"
+      "https://github.com/nextstrain/rsv/issues"
     ],
     "organizations": [
       "Nextstrain"
     ],
     "authors": [
       "Nextstrain team <https://nextstrain.org>"
     ]
+  },
+  "attributes": {
+    "name": "RSV-A",
+    "reference accession": "EPI_ISL_412866",
+    "reference name": "hRSV/A/England/397/2017"
+  },
+  "version": {
+    "tag": "unreleased"
   }
 }