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Snippy Phylogenomics

Core SNPs are identified by snippy-core. gubbins is used to identify and filter recombinant loci.

flowchart TD
  snippy_dirs[snippy_dirs] --> snippy_core[snippy_core]
  ref[reference.fasta] --> snippy_core
  snippy_core --> core_aln[core.aln]
  snippy_core --> core_variants[core.vcf]
  snippy_core --> core_stats[core.vcf]
  snippy_core --> full_alignment[core.full.aln]
  snippy_core --> clean_full_alignment[clean.full.aln]
  clean_full_alignment -->|process WITH gubbins| gubbins(gubbins)
  gubbins --> filtered_polymorphic_sites[gubbins.filtered_polymorphic_sites.fasta]
  gubbins --> recombination_predictions_gff[gubbins.recombination_predictions.gff]
  gubbins --> per_branch_statistics[gubbins.per_branch_statistics.tsv]
  clean_full_alignment --> |process WITHOUT gubbins| snp_sites
  snp_sites -->  snp_sites_out[clean.core.aln]
  filtered_polymorphic_sites --> snp_sites
  snp_sites_out --> iqtree
  iqtree --> iqtree_out[alignment.treefile]
  snp_sites_out --> snp_dists
  snp_dists --> snp_dists_out[alignment.distances.tsv]
  iqtree_out --> shiptv
  shiptv --> tree_html[tree.html]
Loading

Note: the process WITHOUT gubbins occurs if --skip_gubbins is true. This parameter should be used when your input has only 2 samples as gubbins requires a minimum of 3 samples.

Inputs

  • --snippy_dirs:
  • --ref: A reference .fasta file

Usage

nextflow run BCCDC-PHL/snippy-core-phylogenomics \
  --snippy_dirs </path/to/snippy_output_dirs> \
  --ref ref.fa \
  [--mask mask.bed] \
  --outdir outdir

Outputs

Provenance

In the output directory, a provenance file will be written with the following format:

- pipeline_name: BCCDC-PHL/snippy-core-phylogenomics
  pipeline_version: 0.1.2
  nextflow_session_id: 15245f59-7acc-4a0d-88ee-2232ddad329f
  nextflow_run_name: zen_goldwasser
  timestamp_analysis_start: 2024-11-21T14:59:18.014789-08:00
- process_name: snippy_core
  tools:
    - tool_name: snippy_core
      tool_version: 4.6.0
      parameters:
        - parameter: --ref
          value: H37Rv_NC000962.3.fasta
        - parameter: --mask
          value: mask.bed
- process_name: gubbins
  tools:
    - tool_name: gubbins
      tool_version: 3.3.1
      parameters:
        - parameter: --threads
          value: 8
        - parameter: -p
          value: gubbins
- process_name: snp_sites
  tools:
    - tool_name: snp_sites
      tool_version: 2.5.1
      parameters:
        - parameter: -c
          value: gubbins.filtered_polymorphic_sites.fasta
- process_name: iqtree
  tools:
    - tool_name: iqtree
      tool_version: 2.3.6
      parameters:
        - parameter: -nt
          value: 16
        - parameter: -fconst
          value: 0,0,0,0
        - parameter: -s
          value: clean.core.aln
        - parameter: -st
          value: DNA
        - parameter: -m
          value: GTR+G
- process_name: shiptv
  tools:
    - tool_name: shiptv
      tool_version: 0.4.1
      parameters:
        - parameter: -n
          value: clean.core.aln.treefile
        - parameter: -0
          value: clean.core.aln.treefile.html