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Augur is a bioinformatics toolkit to track evolution from sequence and serological data. It provides a collection of commands which are designed to be composable into larger processing pipelines. Augur originated as part of Nextstrain, an open-source project to harness the scientific and public health potential of pathogen genome data.



See versions of augur which are available:

$ module avail augur

Load one version into your environment and run it:

$ module load augur/11.2.0
$ augur

To familiarize yourself with the Augur workflow you should try their sample ncov data, for example:

$ interactive -c 4 -w compute05 -J nextstrain-augur
$ git clone /var/scratch/aorth-ncov
$ cd /var/scratch/aorth-ncov
$ module load augur/11.2.0
$ gzip -d -c data/example_sequences.fasta.gz > data/example_sequences.fasta
$ snakemake --cores 4 --profile ./my_profiles/getting_started

For more information see the Augur documentation.


Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/augur/11.2.0
$ sudo chown aorth:aorth /export/apps/augur/11.2.0
$ module load python/3.7
$ python -m venv /export/apps/augur/11.2.0/.venv
$ source /export/apps/augur/11.2.0/.venv/bin/activate
$ pip install nextstrain-augur==11.2.0
$ pip install nextstrain-cli
$ pip install snakemake
$ module load mafft/7.313 RAxML/8.2.12 fasttree/2.1.11 iqtree/1.6.12 vcftools/0.1.16 nextalign/0.1.7
$ nextstrain setup-check
$ sudo chown -R root:root /export/apps/augur/11.2.0
augur-software.txt · Last modified: 2021/03/15 12:32 by aorth