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Merge pull request #20 from nextstrain/add-N450-tree
Make tree for 450bp of the N gene ("N450")
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‎CHANGES.md‎

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# CHANGELOG
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* 1 April 2024: Create a tree using the 450 nucleotides encoding the carboxyl-terminal 150 amino acids of the nucleoprotein (N450), which is highly represented on NCBI for measles. [PR #20](https://github.com/nextstrain/measles/pull/20)
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* 15 March 2024: Connect ingest and phylogenetic workflows to follow the pathogen-repo-guide by uploading ingest output to S3, downloading ingest output from S3 to phylogenetic directory, using "accession" column as the ID column, and using a color scheme that matches the new region name format. [PR #19](https://github.com/nextstrain/measles/pull/19)
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* 1 March 2024: Add phylogenetic directory to follow the pathogen-repo-guide, and update the CI workflow to match the new file structure. [PR #18](https://github.com/nextstrain/measles/pull/18)
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* 14 February 2024: Add ingest directory from pathogen-repo-guide and make measles-specific modifications. [PR #10](https://github.com/nextstrain/measles/pull/10)

‎phylogenetic/Snakefile‎

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genes = ['N450', 'genome']
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configfile: "defaults/config.yaml"
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rule all:
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input:
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auspice_json = "auspice/measles.json",
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auspice_json = expand("auspice/measles_{gene}.json", gene=genes)
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include: "rules/prepare_sequences.smk"
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include: "rules/prepare_sequences_N450.smk"
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include: "rules/construct_phylogeny.smk"
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include: "rules/annotate_phylogeny.smk"
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include: "rules/export.smk"

‎phylogenetic/defaults/auspice_config.json‎

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"title": "Date",
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"type": "continuous"
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},
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{
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"key": "author",
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"title": "Author",
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"type": "categorical"
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},
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{
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"key": "country",
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"title": "Country",
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"country",
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"region",
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"author"
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],
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"metadata_columns": [
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"author"
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]
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}

‎phylogenetic/defaults/auspice_config_N450.json‎

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{
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"title": "Real-time tracking of measles virus evolution",
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"maintainers": [
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{"name": "Kim Andrews", "url": "https://bedford.io/team/kim-andrews/"},
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{"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}
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],
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"build_url": "https://github.com/nextstrain/measles",
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"colorings": [
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{
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"key": "gt",
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"title": "Genotype",
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"type": "categorical"
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},
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{
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"key": "num_date",
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"title": "Date",
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"type": "continuous"
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},
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{
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"key": "country",
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"title": "Country",
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"type": "categorical"
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},
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{
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"key": "region",
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"title": "Region",
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"type": "categorical"
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}
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],
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"geo_resolutions": [
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"country",
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"region"
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],
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"display_defaults": {
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"map_triplicate": true
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},
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"filters": [
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"country",
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"region",
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"author"
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],
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"metadata_columns": [
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"author"
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]
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}

‎phylogenetic/defaults/colors.tsv‎

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region Europe #BEBB48
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region South America #E29E39
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region North America #E2562B
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country india #511EA8
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country china #4333BE
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country vietnam #3F4ECB
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country south korea #4169CF
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country japan #4682C9
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country australia #4F96BB
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country new zealand #5AA5A8
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country russia #68AF92
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country gambia #78B77D
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country sudan #8BBB6A
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country morocco #9EBE59
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country italy #B3BD4D
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country germany #C5B945
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country france #D5B03F
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country netherlands #E0A23A
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country united kingdom #E68D36
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country brazil #E67231
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country usa #E1502A
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country canada #DC2F24

‎phylogenetic/defaults/config.yaml‎

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files:
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exclude: "defaults/dropped_strains.txt"
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reference: "defaults/measles_reference.gb"
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reference_N450: "defaults/measles_reference_N450.gb"
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reference_N450_fasta: "defaults/measles_reference_N450.fasta"
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colors: "defaults/colors.tsv"
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auspice_config: "defaults/auspice_config.json"
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auspice_config_N450: "defaults/auspice_config_N450.json"
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filter:
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group_by: "country year month"
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sequences_per_group: 20
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min_date: 1950
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min_length: 5000
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filter_N450:
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group_by: "country year"
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subsample_max_sequences: 3000
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min_date: 1950
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min_length: 400
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refine:
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coalescent: "opt"
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date_inference: "marginal"

‎phylogenetic/defaults/measles_reference_N450.fasta‎

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>lcl|NC_001498.1_cds_NP_056918.1_1 [gene=N] [locus_tag=MeVgp1] [db_xref=GeneID:1489804] [protein=nucleocapsid protein] [protein_id=NP_056918.1] [location=1233..1682] [gbkey=CDS]
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GTCAGTTCCACATTGGCATCCGAACTCGGTATCACTGCCGAGGATGCAAGGCTTGTTTCAGAGAT
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TGCAATGCATACTACTGAGGACAGGATCAGTAGAGCGGTCGGACCCAGACAAGCCCAAGTGTCATTTCTA
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CACGGTGATCAAAGTGAGAATGAGCTACCAGGATTGGGGGGCAAGGAAGATAGGAGGGTCAAACAGGGTC
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GGGGAGAAGCCAGGGAGAGCTACAGAGAAACCGGGTCCAGCAGAGCAAGTGATGCGAGAGCTGCCCATCC
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TCCAACCAGCATGCCCCTAGACATTGACACTGCATCGGAGTCAGGCCAAGATCCGCAGGACAGTCGAAGG
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TCAGCTGACGCCCTGCTCAGGCTGCAAGCCATGGCAGGAATCTTGGAAGAACAAGGCTCAGACACGGACA
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CCCCTAGGGTATACAATGACAGAGATCTTCTAGAC

‎phylogenetic/defaults/measles_reference_N450.gb‎

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LOCUS NC_001498 450 bp cRNA linear VRL 13-AUG-2018
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DEFINITION Measles virus, complete genome.
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ACCESSION NC_001498 REGION: 1233..1682
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VERSION NC_001498.1
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DBLINK Project: 15025
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BioProject: PRJNA485481
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KEYWORDS RefSeq.
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SOURCE Measles morbillivirus
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ORGANISM Measles morbillivirus
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Viruses; Riboviria; Orthornavirae; Negarnaviricota;
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Haploviricotina; Monjiviricetes; Mononegavirales; Paramyxoviridae;
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Orthoparamyxovirinae; Morbillivirus; Morbillivirus hominis.
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REFERENCE 1 (sites)
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AUTHORS Rima,B.K. and Duprex,W.P.
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TITLE The measles virus replication cycle
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JOURNAL Curr. Top. Microbiol. Immunol. 329, 77-102 (2009)
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PUBMED 19198563
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REFERENCE 2
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AUTHORS Takeuchi,K., Miyajima,N., Kobune,F. and Tashiro,M.
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TITLE Comparative nucleotide sequence analyses of the entire genomes of
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B95a cell-isolated and vero cell-isolated measles viruses from the
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same patient
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JOURNAL Virus Genes 20 (3), 253-257 (2000)
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PUBMED 10949953
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REFERENCE 3 (bases 1 to 450)
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CONSRTM NCBI Genome Project
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TITLE Direct Submission
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JOURNAL Submitted (01-AUG-2000) National Center for Biotechnology
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Information, NIH, Bethesda, MD 20894, USA
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REFERENCE 4 (bases 1 to 450)
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AUTHORS Takeuchi,K., Tanabayashi,K. and Tashiro,M.
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TITLE Direct Submission
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JOURNAL Submitted (10-JUL-1998) Kaoru Takeuchi, National Institute of
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Infectious Diseases, Viral Disease and Vaccine Contorol; 4-7-1
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Gakuen, Musashi-murayama, Tokyo 208-0011, Japan
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(E-mail:[email protected], Tel:81-42-561-0771(ex.530),
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Fax:81-42-567-5631)
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COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The
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reference sequence was derived from AB016162.
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Sequence updated (21-Jul-1998)
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Sequence updated (11-Dec-1998).
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COMPLETENESS: full length.
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FEATURES Location/Qualifiers
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source 1..450
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/organism="Measles morbillivirus"
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/mol_type="viral cRNA"
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/strain="Ichinose-B95a"
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/db_xref="taxon:11234"
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CDS <1..>450
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/gene="N"
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/codon_start=1
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/product="nucleocapsid protein"
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/protein_id="NP_056918.1"
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/db_xref="GeneID:1489804"
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/translation="VSSTLASELGITAEDAR
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LVSEIAMHTTEDRISRAVGPRQAQVSFLHGDQSENELPGLGGKEDRRVKQGRGEARES
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YRETGSSRASDARAAHPPTSMPLDIDTASESGQDPQDSRRSADALLRLQAMAGILEEQ
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GSDTDTPRVYNDRDLLD"
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ORIGIN
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1 gtcagttcca cattggcatc cgaactcggt atcactgccg aggatgcaag gcttgtttca
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61 gagattgcaa tgcatactac tgaggacagg atcagtagag cggtcggacc cagacaagcc
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121 caagtgtcat ttctacacgg tgatcaaagt gagaatgagc taccaggatt ggggggcaag
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181 gaagatagga gggtcaaaca gggtcgggga gaagccaggg agagctacag agaaaccggg
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241 tccagcagag caagtgatgc gagagctgcc catcctccaa ccagcatgcc cctagacatt
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301 gacactgcat cggagtcagg ccaagatccg caggacagtc gaaggtcagc tgacgccctg
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361 ctcaggctgc aagccatggc aggaatcttg gaagaacaag gctcagacac ggacacccct
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421 agggtataca atgacagaga tcttctagac
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//
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‎phylogenetic/rules/annotate_phylogeny.smk‎

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rule ancestral:
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"""Reconstructing ancestral sequences and mutations"""
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input:
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tree = "results/tree.nwk",
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alignment = "results/aligned.fasta"
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tree = "results/{gene}/tree.nwk",
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alignment = "results/{gene}/aligned.fasta"
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output:
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node_data = "results/nt_muts.json"
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node_data = "results/{gene}/nt_muts.json"
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params:
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inference = config["ancestral"]["inference"]
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shell:
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rule translate:
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"""Translating amino acid sequences"""
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input:
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tree = "results/tree.nwk",
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node_data = "results/nt_muts.json",
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reference = config["files"]["reference"]
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tree = "results/{gene}/tree.nwk",
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node_data = "results/{gene}/nt_muts.json",
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reference = lambda wildcard: "defaults/measles_reference.gb" if wildcard.gene in ["genome"] else "defaults/measles_reference_{gene}.gb"
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output:
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node_data = "results/aa_muts.json"
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node_data = "results/{gene}/aa_muts.json"
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shell:
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"""
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augur translate \

‎phylogenetic/rules/construct_phylogeny.smk‎

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rule tree:
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"""Building tree"""
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input:
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alignment = "results/aligned.fasta"
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alignment = "results/{gene}/aligned.fasta"
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output:
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tree = "results/tree_raw.nwk"
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tree = "results/{gene}/tree_raw.nwk"
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shell:
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"""
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augur tree \
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- filter tips more than {params.clock_filter_iqd} IQDs from clock expectation
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"""
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input:
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tree = "results/tree_raw.nwk",
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alignment = "results/aligned.fasta",
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tree = "results/{gene}/tree_raw.nwk",
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alignment = "results/{gene}/aligned.fasta",
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metadata = "data/metadata.tsv"
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output:
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tree = "results/tree.nwk",
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node_data = "results/branch_lengths.json"
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tree = "results/{gene}/tree.nwk",
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node_data = "results/{gene}/branch_lengths.json"
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params:
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coalescent = config["refine"]["coalescent"],
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date_inference = config["refine"]["date_inference"],
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--coalescent {params.coalescent} \
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--date-confidence \
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--date-inference {params.date_inference} \
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--clock-filter-iqd {params.clock_filter_iqd}
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--clock-filter-iqd {params.clock_filter_iqd} \
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--stochastic-resolve
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"""
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