33.0.0

Augur Container

Main tool: Augur

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.

Additional dependencies

• fasttree 2.1.11-2
• python 3.11.13
• iqtree 2.0.7+dfsg-1+b2
• mafft 7.505-1
• raxml 8.2.13+dfsg-2+b1
• vcftools 0.1.16-3+b1
• seqkit 2.12.0

Additional tools installed via pip:

Package                   Version
------------------------- -----------
attrs                     25.4.0
bcbio-gff                 0.7.1
biopython                 1.86
contourpy                 1.3.3
cvxopt                    1.3.3
cycler                    0.12.1
fonttools                 4.61.1
isal                      1.8.0
isodate                   0.7.2
jsonschema                4.26.0
jsonschema-specifications 2025.9.1
kiwisolver                1.4.9
matplotlib                3.10.8
networkx                  3.6.1
nextstrain-augur          33.0.0
numpy                     2.4.2
packaging                 26.0
pandas                    2.3.3
phylo-treetime            0.11.4
pillow                    12.1.1
pip                       24.0
pyfastx                   2.3.0
pyparsing                 3.3.2
python-calamine           0.6.1
python-dateutil           2.9.0.post0
pytz                      2025.2
PyYAML                    6.0.3
referencing               0.37.0
rpds-py                   0.30.0
scipy                     1.17.0
setuptools                79.0.1
six                       1.17.0
typing_extensions         4.15.0
tzdata                    2025.3
wheel                     0.45.1
xopen                     2.0.2
zlib-ng                   1.0.0
zstandard                 0.25.0

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-sequences results/filtered.fasta \
  --group-by country year month \
  --sequences-per-group 20 \
  --min-date 2012

Better documentation can be found here.