Augur
Introduction
Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.
For more information, please check its website: https://biocontainers.pro/tools/augur and its home page on Github.
Versions
14.0.0
15.0.0
Commands
augur
Module
You can load the modules by:
module load biocontainers
module load augur
Example job
Warning
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Augur on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=augur
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers augur
mkdir -p results
augur index --sequences zika-tutorial/data/sequences.fasta \
--output results/sequence_index.tsv
augur filter --sequences zika-tutorial/data/sequences.fasta \
--sequence-index results/sequence_index.tsv \
--metadata zika-tutorial/data/metadata.tsv \
--exclude zika-tutorial/config/dropped_strains.txt \
--output results/filtered.fasta \
--group-by country year month \
--sequences-per-group 20 \
--min-date 2012
augur align --sequences results/filtered.fasta \
--reference-sequence zika-tutorial/config/zika_outgroup.gb \
--output results/aligned.fasta \
--fill-gaps
augur tree --alignment results/aligned.fasta \
--output results/tree_raw.nwk
augur refine --tree results/tree_raw.nwk \
--alignment results/aligned.fasta \
--metadata zika-tutorial/data/metadata.tsv \
--output-tree results/tree.nwk \
--output-node-data results/branch_lengths.json \
--timetree \
--coalescent opt \
--date-confidence \
--date-inference marginal \
--clock-filter-iqd 4