Pipeline components for real-time phylodynamic analysis

Using Fasta Input

If you would like to run augur on viral data, or bacterial SNP data, you probably would like to start with Fasta sequence data.

Sequence data

Your sequence data should

  • consist of homologous sequences that can be aligned unambiguously
  • needs to contain sufficient diversity to allow reliable tree reconstruction
  • should be of similar length. Mixing short sequences (300bp) with much longer ones (10000bp) often yields unexpected results.