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Augurlinos: a collection of modules for molecular epidemiology

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.

Quickstart

Put a zika.fasta into zika/data and run

snakemake --snakefile zika/zika_snake export

Requirments

• python 2.7
• numpy, biopython, scipy
• treetime

Structure

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

ToDos

• 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.