26.0.0

Augur Container

Main tool: Augur

Additional tools:

• mafft 7.505
• iqtree2 2.0.7
• raxml 8.2.12
• fasttree 2.1.11
• vcftools 0.1.16
• biopython 1.84
• matplotlib 3.9.2
• numpy 1.26.4
• pandas 1.5.3
• phylo-treetime 0.11.4
• python 3.11.10
• scipy 1.14.1

Definition: One held to foretell events by omens.

Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data. It provides a collection of commands which are designed to be composable into larger processing pipelines.

The output of augur is a series of JSONs that can be used to visualize your results using Auspice.

Note: Auspice is a different tool.

Example Usage

augur index --sequences sequences.fasta --output sequence_index.tsv

augur filter \
  --sequences data/sequences.fasta \
  --sequence-index results/sequence_index.tsv \
  --metadata data/metadata.tsv \
  --exclude config/dropped_strains.txt \
  --output results/filtered.fasta \
  --group-by country year month \
  --sequences-per-group 20 \
  --min-date 2012

Better documentation can be found here.