Nextstrain is a powerful pathogen surveillance tool that creates interactive visualizations to explore curated datasets and analyses. It is composed of two main programs Augur and Auspice. Augur is a package of bioinformatic tools that creates the JSON files that are used by a web-based interactive visualization program, Auspice. Nextstrain defines a ‘build’ as ‘A sequence of commands, parameters and input files which work together to reproducibly execute bioinformatic analyses and generate a dataset for visualization with Auspice.’ This Nextflow workflow aims at making and developing these ‘Builds’ simple and easy. Many Nextstrain projects currently rely on ‘snakemake’ which provides a good example of what Nextstain_Build is trying to do. Example
Nextstrain_Build will create a basic phylogenetic tree from a multi-sequence alignment by just providing a --multi_fasta file and --metadata file in .tsv format. But this is just a starting point for building out a much more detailed analysis. Producing a time resolved tree, finding ancestral traits and sequences, and identifying amino-acid mutations can be included by changing these parameters to true:
params.time_resolved = false
params.construct_ancestral_traits = false
params.construct_ancestral_sequences = false
params.indentify_aa_mutations = false
Additional config files can also be passed that allow the user to add colors, locations, and edit the Auspice display in detail.
params.colors = false
params.lat_longs = false
params.auspice_config = false
Details on the format for the auspice config file.
- Create module that verifies the fasta file and metadata file
- Possibly expand to verify all other incoming config files