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Augur Container

Main tool: Augur

Additional tools:

  • biopython 1.85
  • fasttree 2.1.11
  • iqtree2 2.0.7
  • mafft 7.505
  • matplotlib 3.10.1
  • numpy 1.26.4
  • pandas 2.2.3
  • python 3.11.11
  • raxml 8.2.12
  • scipy 1.15.1
  • vcftools 0.1.16

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.