github.com/CDPHE/COVIDalignmentPhylogeny

Automatic Tools and Workflows
1

COVIDalignmentPhylogeny

Takes the consensus fasta SARS-CoV-2 genome assembly outputs of IlluminaPreprocessAssembly.wdl and NanoporeGuppyAssembly.wdl and a reference genome which should be stored in your Terra workspace data and does the following:

  1. concatenates the input fasta genome and the references into a multifasta
  2. aligns the sequences using mafft
  3. generates a pairwise distance matrix with snp-dists
  4. generates a phylogeny with iqtree
  5. exports the outputs to your chosen google
This is a companion discussion topic for the original entry at github.com/CDPHE/COVIDalignmentPhylogeny