This repo was a prototype of how to strip down augur into a series of interacting modules. All development has moved to the augur repository.

Put a zika.fasta into zika/data and run

snakemake --snakefile zika/zika_snake export

• python 2.7
• numpy, biopython, scipy
• treetime

Each build should have a Snakefile. The example zika/zika_snake requires a fasta file with zika sequence (fauna output) and an annotated reference sequence in genbank format. Each feature that should be translated needs a "locus_tag" which will be used to name the translation.

Different steps of a build produce standard files (alignments in fasta format, tree in newick format, tables as tsv) on which subsequent steps rely. The final step exports a jsons for auspice

• meta.json is not yet created
• frequencies and titers at not yet done (easy)
• support for multiple segments is missing
• prepare doesn't do anything meaningful.