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Overview

The Snippy_Streamline_FASTA workflow is an all-in-one approach to generating a reference-based phylogenetic tree and associated SNP-distance matrix. The workflow can be run in multiple ways with options for

• The reference genome to be provided by the user, or automatically selected using the Centroid task and Assembly_Fetch sub-workflow to find a close reference genome to your dataset
• The phylogeny to be generated by optionally
  • masking user-specified regions of the genome (providing a bed file to snippy_core_bed)
  • producing either a core or pan-genome phylogeny and SNP-matrix (core_genome; default = true)
  • masking recombination detected by gubbins, or not (use_gubbins; default=true)
  • choosing the nucleotide substitution (by specifying iqtree2_model), or allowing IQ-Tree’s ModelFinder to identify the best model for your dataset (default)

<aside> ℹ️ Sequencing data used in the Snippy_Streamline_FASTA workflow must:

• Be assembled genomes in FASTA format
• Be generated by unbiased whole genome shotgun sequencing
• Pass appropriate QC thresholds for the taxa to ensure that the assemblies represent reasonably complete genomes that are free of contamination from other taxa or cross-contamination of the same taxon.
• If masking recombination with Gubbins, input data should represent complete genomes from the same strain/lineage (e.g. MLST) that share a recent common ancestor. </aside>

<aside> ⚠️ If reference genomes have multiple contigs, they will not be compatible with using Gubbins to mask recombination in the phylogenetic tree. The automatic selection of a reference genome by the workflow may result in a reference with multiple contigs. In this case, an alternative reference genome should be sought.

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Inputs

Snippy_Streamline_FASTA Inputs

Outputs

Snippy_Streamline_FASTA Outputs

References

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