mpox/phylogenetic/defaults/hmpxv1_big/config.yaml at bb1144174e777509b1284c2e2d8c3fc05116cd6a · nextstrain/mpox · GitHub

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reference: "defaults/reference.fasta"
genome_annotation: "defaults/genome_annotation.gff3"
genbank_reference: "defaults/reference.gb"
exclude: "defaults/exclude.txt"
clades: "defaults/clades.tsv"
lat_longs: "defaults/lat_longs.tsv"
color_ordering: "defaults/color_ordering.tsv"
color_scheme: "defaults/color_schemes.tsv"
auspice_config: "defaults/hmpxv1_big/auspice_config.json"
description: "defaults/description.md"
tree_mask: "defaults/tree_mask.tsv"

# Use `accession` as the ID column since `strain` currently contains duplicates¹.
# ¹ https://github.com/nextstrain/mpox/issues/33
strain_id_field: "accession"

build_name: "hmpxv1_big"
auspice_name: "mpox_lineage-B.1"

filter:
  min_date: 2022
  min_length: 180000
  query: "(QC_rare_mutations == 'good' | QC_rare_mutations == 'mediocre')"

subsample:
  samples:
    b1:
      group_by:
        - year
        - month
        - country
      max_sequences: 5000
      exclude_where:
        - outbreak!=hMPXV-1
        - clade!=IIb
        - lineage=A
        - lineage=A.1
        - lineage=A.1.1
        - lineage=A.2
        - lineage=A.2.1
        - lineage=A.2.2
        - lineage=A.2.3
        - lineage=A.3
      include:
        - defaults/hmpxv1_big/include.txt

## align
max_indel: 10000
seed_spacing: 1000

## treefix
fix_tree: true
treefix_root: "OP890401"

## refine
timetree: true
root: "OP890401"
clock_rate: 5.7e-5
clock_std_dev: 2e-5
divergence_units: "mutations"

traits:
  columns: []
  sampling_bias_correction: 3

## recency
recency: true

mask:
  from_beginning: 800
  from_end: 6422
  maskfile: "defaults/mask.bed"