The concept of a ‘build’
Nextstrain’s focus on providing a real-time snapshot of evolving pathogen populations necessitates a reproducible analysis that can be rerun when new sequences are available. The individual steps necessary to repeat analysis together comprise a “build”.
Because no two datasets or pathogens are the same, we build Augur to be flexible and suitable for different analyses. The individual Augur commands are composable, and can be mixed and matched with other scripts as needed. These steps, taken together, are what we refer to as a “build”.
The Zika virus tutorial describes a build which contains the following steps:
Prepare pathogen sequences and metadata
Construct a phylogeny from aligned sequences
Annotate the phylogeny with inferred ancestral pathogen dates, sequences, and traits
Export the annotated phylogeny and corresponding metadata into auspice-readable format
and each of these can be run via a separate
If you look at the other tutorials, each one uses a slightly different combination of
augur commands depending on the pathogen.
While it is possible to run a build by running each of the individual steps, we typically group these together into a make-type file. Snakemake is “a tool to create reproducible and scalable data analyses… via a human-readable, Python-based language.”
Snakemake is installed as part of the conda environment or the docker container. If you ever see a build which has a “Snakefile” then you can run this by typing
snakemake --cores 1or
nextstrain build --cpus 1 ., respectively.