Nextstrain_Build

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

Usage

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.

To Do

• Create module that verifies the fasta file and metadata file
  • Possibly expand to verify all other incoming config files