4.7. augur_from_assemblies¶
Align assemblies, build trees, and convert to json representation suitable for Nextstrain visualization. See https://nextstrain.org/docs/getting-started/ and https://nextstrain-augur.readthedocs.io/en/stable/
4.7.1. Inputs¶
4.7.1.1. Required inputs¶
augur_from_assemblies.assembly_fastas
Array[File]+ — Default: None
Set of assembled genomes to align and build trees. These must represent a single chromosome/segment of a genome only. Fastas may be one-sequence-per-individual or a concatenated multi-fasta (unaligned) or a mixture of the two. They may be compressed (gz, bz2, zst, lz4), uncompressed, or a mixture.
augur_from_assemblies.export_auspice_json.auspice_config
File — Default: None
???
augur_from_assemblies.min_unambig_genome
Int — Default: None
Minimum number of called bases in genome to pass prefilter.
augur_from_assemblies.ref_fasta
File — Default: None
A reference assembly (not included in assembly_fastas) to align assembly_fastas against. Typically from NCBI RefSeq or similar.
augur_from_assemblies.sample_metadata_tsvs
Array[File]+ — Default: None
Tab-separated metadata file that contain binning variables and values. Must contain all samples: output will be filtered to the IDs present in this file.
augur_from_assemblies.translate_augur_tree.genbank_gb
File — Default: None
???
4.7.1.2. Other inputs¶
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augur_from_assemblies.ancestral_traits.confidence
Boolean — Default: true
???
augur_from_assemblies.ancestral_traits.disk_size
Int — Default: 750
???
augur_from_assemblies.ancestral_traits.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_assemblies.ancestral_traits.machine_mem_gb
Int — Default: 32
???
augur_from_assemblies.ancestral_traits.sampling_bias_correction
Float? — Default: None
???
augur_from_assemblies.ancestral_traits.weights
File? — Default: None
???
augur_from_assemblies.ancestral_traits_to_infer
Array[String]? — Default: None
A list of metadata traits to use for ancestral node inference (see https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/traits.html). Multiple traits may be specified; must correspond exactly to column headers in metadata file. Omitting these values will skip ancestral trait inference, and ancestral nodes will not have estimated values for metadata.
augur_from_assemblies.ancestral_tree.disk_size
Int — Default: 300
???
augur_from_assemblies.ancestral_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_assemblies.ancestral_tree.infer_ambiguous
Boolean — Default: false
???
augur_from_assemblies.ancestral_tree.inference
String — Default: "joint"
???
augur_from_assemblies.ancestral_tree.keep_ambiguous
Boolean — Default: false
???
augur_from_assemblies.ancestral_tree.keep_overhangs
Boolean — Default: false
???
augur_from_assemblies.ancestral_tree.output_vcf
File? — Default: None
???
augur_from_assemblies.ancestral_tree.vcf_reference
File? — Default: None
???
augur_from_assemblies.assign_clades_to_nodes.disk_size
Int — Default: 300
???
augur_from_assemblies.assign_clades_to_nodes.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_assemblies.augur_mask_sites.disk_size
Int — Default: 750
???
augur_from_assemblies.augur_mask_sites.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_assemblies.augur_mask_sites.mask_bed
File? — Default: None
???
augur_from_assemblies.clades_tsv
File? — Default: None
A TSV file containing clade mutation positions in four columns: [clade gene site alt]; see: https://nextstrain.org/docs/tutorials/defining-clades
augur_from_assemblies.derived_cols.disk_size
Int — Default: 50
???
augur_from_assemblies.derived_cols.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
augur_from_assemblies.derived_cols.lab_highlight_loc
String? — Default: None
This option copies the 'originating_lab' and 'submitting_lab' columns to new ones including a prefix, but only if they match certain criteria. The value of this string must be of the form prefix;col_header=value:col_header=value. For example, 'MA;country=USA:division=Massachusetts' will copy the originating_lab and submitting_lab columns to MA_originating_lab and MA_submitting_lab, but only for those rows where country=USA and division=Massachusetts.
augur_from_assemblies.derived_cols.table_map
Array[File] — Default: []
Mapping tables. Each mapping table is a tsv with a header. The first column is the output column name for this mapping (it will be created or overwritten). The subsequent columns are matching criteria. The value in the first column is written to the output column. The exception is in the case where all match columns are '*' -- in this case, the value in the first column is the column header name to copy over.
augur_from_assemblies.draft_augur_tree.cpus
Int — Default: 64
???
augur_from_assemblies.draft_augur_tree.disk_size
Int — Default: 1250
???
augur_from_assemblies.draft_augur_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_assemblies.draft_augur_tree.exclude_sites
File? — Default: None
???
augur_from_assemblies.draft_augur_tree.machine_mem_gb
Int — Default: 32
???
augur_from_assemblies.draft_augur_tree.method
String — Default: "iqtree"
???
augur_from_assemblies.draft_augur_tree.substitution_model
String — Default: "GTR"
???
augur_from_assemblies.draft_augur_tree.tree_builder_args
String? — Default: None
???
augur_from_assemblies.draft_augur_tree.vcf_reference
File? — Default: None
???
augur_from_assemblies.export_auspice_json.color_by_metadata
Array[String]? — Default: None
???
augur_from_assemblies.export_auspice_json.colors_tsv
File? — Default: None
???
augur_from_assemblies.export_auspice_json.description_md
File? — Default: None
???
augur_from_assemblies.export_auspice_json.disk_size
Int — Default: 300
???
augur_from_assemblies.export_auspice_json.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_assemblies.export_auspice_json.geo_resolutions
Array[String]? — Default: None
???
augur_from_assemblies.export_auspice_json.include_root_sequence
Boolean — Default: true
???
augur_from_assemblies.export_auspice_json.lat_longs_tsv
File? — Default: None
???
augur_from_assemblies.export_auspice_json.machine_mem_gb
Int — Default: 64
???
augur_from_assemblies.export_auspice_json.maintainers
Array[String]? — Default: None
???
augur_from_assemblies.export_auspice_json.out_basename
String — Default: basename(basename(tree,".nwk"),"_timetree")
???
augur_from_assemblies.export_auspice_json.title
String? — Default: None
???
augur_from_assemblies.filter_sequences_by_length.disk_size
Int — Default: 750
???
augur_from_assemblies.filter_sequences_by_length.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
augur_from_assemblies.mafft.cpus
Int — Default: 64
???
augur_from_assemblies.mafft.disk_size
Int — Default: 750
???
augur_from_assemblies.mafft.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.20.2"
???
augur_from_assemblies.mafft.keep_length
Boolean — Default: true
???
augur_from_assemblies.mafft.large
Boolean — Default: false
???
augur_from_assemblies.mafft.mem_size
Int — Default: 500
???
augur_from_assemblies.mafft.memsavetree
Boolean — Default: false
???
augur_from_assemblies.mafft.remove_reference
Boolean — Default: false
???
augur_from_assemblies.make_snps_vcf
Boolean — Default: false
???
augur_from_assemblies.prefilter.disk_size
Int — Default: 750
???
augur_from_assemblies.prefilter.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_assemblies.prefilter.exclude
File? — Default: None
???
augur_from_assemblies.prefilter.exclude_where
Array[String]? — Default: None
???
augur_from_assemblies.prefilter.group_by
String? — Default: None
???
augur_from_assemblies.prefilter.include
File? — Default: None
???
augur_from_assemblies.prefilter.include_where
Array[String]? — Default: None
???
augur_from_assemblies.prefilter.max_date
Float? — Default: None
???
augur_from_assemblies.prefilter.min_date
Float? — Default: None
???
augur_from_assemblies.prefilter.min_length
Int? — Default: None
???
augur_from_assemblies.prefilter.non_nucleotide
Boolean — Default: true
???
augur_from_assemblies.prefilter.priority
File? — Default: None
???
augur_from_assemblies.prefilter.sequences_per_group
Int? — Default: None
???
augur_from_assemblies.prefilter.subsample_seed
Int? — Default: None
???
augur_from_assemblies.refine_augur_tree.branch_length_inference
String? — Default: None
???
augur_from_assemblies.refine_augur_tree.clock_filter_iqd
Int? — Default: 4
???
augur_from_assemblies.refine_augur_tree.clock_rate
Float? — Default: None
???
augur_from_assemblies.refine_augur_tree.clock_std_dev
Float? — Default: None
???
augur_from_assemblies.refine_augur_tree.coalescent
String? — Default: None
???
augur_from_assemblies.refine_augur_tree.covariance
Boolean? — Default: None
???
augur_from_assemblies.refine_augur_tree.date_confidence
Boolean — Default: true
???
augur_from_assemblies.refine_augur_tree.date_inference
String? — Default: "marginal"
???
augur_from_assemblies.refine_augur_tree.disk_size
Int — Default: 750
???
augur_from_assemblies.refine_augur_tree.divergence_units
String? — Default: "mutations"
???
augur_from_assemblies.refine_augur_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_assemblies.refine_augur_tree.gen_per_year
Int? — Default: None
???
augur_from_assemblies.refine_augur_tree.keep_polytomies
Boolean — Default: false
???
augur_from_assemblies.refine_augur_tree.keep_root
Boolean — Default: true
???
augur_from_assemblies.refine_augur_tree.machine_mem_gb
Int — Default: 75
???
augur_from_assemblies.refine_augur_tree.precision
Int? — Default: None
???
augur_from_assemblies.refine_augur_tree.root
String? — Default: None
???
augur_from_assemblies.refine_augur_tree.vcf_reference
File? — Default: None
???
augur_from_assemblies.snp_sites.allow_wildcard_bases
Boolean — Default: true
???
augur_from_assemblies.snp_sites.disk_size
Int — Default: 750
???
augur_from_assemblies.snp_sites.docker
String — Default: "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0"
???
augur_from_assemblies.tip_frequencies.censored
Boolean — Default: false
???
augur_from_assemblies.tip_frequencies.disk_size
Int — Default: 200
???
augur_from_assemblies.tip_frequencies.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_assemblies.tip_frequencies.include_internal_nodes
Boolean — Default: false
???
augur_from_assemblies.tip_frequencies.inertia
Float? — Default: None
???
augur_from_assemblies.tip_frequencies.machine_mem_gb
Int — Default: 64
???
augur_from_assemblies.tip_frequencies.max_date
Float? — Default: None
???
augur_from_assemblies.tip_frequencies.method
String — Default: "kde"
???
augur_from_assemblies.tip_frequencies.min_date
Float? — Default: None
???
augur_from_assemblies.tip_frequencies.minimal_frequency
Float? — Default: None
???
augur_from_assemblies.tip_frequencies.narrow_bandwidth
Float? — Default: None
???
augur_from_assemblies.tip_frequencies.out_basename
String — Default: basename(tree,'.nwk')
???
augur_from_assemblies.tip_frequencies.pivot_interval
Int? — Default: None
???
augur_from_assemblies.tip_frequencies.pivot_interval_units
String? — Default: None
???
augur_from_assemblies.tip_frequencies.proportion_wide
Float? — Default: None
???
augur_from_assemblies.tip_frequencies.stiffness
Float? — Default: None
???
augur_from_assemblies.tip_frequencies.wide_bandwidth
Float? — Default: None
???
augur_from_assemblies.translate_augur_tree.disk_size
Int — Default: 300
???
augur_from_assemblies.translate_augur_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_assemblies.translate_augur_tree.genes
File? — Default: None
???
augur_from_assemblies.translate_augur_tree.vcf_reference
File? — Default: None
???
augur_from_assemblies.translate_augur_tree.vcf_reference_output
File? — Default: None
???
augur_from_assemblies.tsv_join.machine_mem_gb
Int — Default: 7
???
augur_from_assemblies.tsv_join.out_suffix
String — Default: ".txt"
???
augur_from_assemblies.tsv_join.prefer_first
Boolean — Default: true
???
augur_from_assemblies.zcat.cpus
Int — Default: 4
???
4.7.2. Outputs¶
augur_from_assemblies.auspice_input_json
File
???
augur_from_assemblies.combined_assemblies
File
???
augur_from_assemblies.keep_list
File
???
augur_from_assemblies.masked_alignment
File
???
augur_from_assemblies.metadata_merged
File
???
augur_from_assemblies.ml_tree
File
???
augur_from_assemblies.multiple_alignment
File
???
augur_from_assemblies.node_data_jsons
Array[File]
???
augur_from_assemblies.root_sequence_json
File
???
augur_from_assemblies.sequences_kept
Int
???
augur_from_assemblies.subsampled_sequences
File
???
augur_from_assemblies.time_tree
File
???
augur_from_assemblies.tip_frequencies_json
File
???
augur_from_assemblies.unmasked_snps
File?
???
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