global19 / seasonal-flu

Scripts. config, and snakefiles for seasonal-flu nextstrain builds

nextstrain.org/flu

This is the Nextstrain build for seasonal influenza viruses, available online at nextstrain.org/flu.

The build encompasses fetching data, preparing it for analysis, doing quality control, performing analyses, and saving the results in a format suitable for visualization (with auspice). This involves running components of Nextstrain such as fauna and augur.

All influenza virus specific steps and functionality for the Nextstrain pipeline should be housed in this repository.

This build is more complicated than other standard nextstrain build because all four currently circulating seasonal influenza lineages (A/H3N2, A/H1N1pdm, B/Vic and B/Yam) are analyzed using the same Snakefile with appropriate wildcards. In addition, we run analyses of both the HA and NA segments of the influenza virus genome and analyze datasets that span different time intervals (eg 2, 3, 6 years).

Furthermore, the Nextstrain analysis of influenza virus evolution also uses antigenic and serological data from different WHO collaborating centers. These antigenic data come in four flavors depending on the assay that passage history of the antigens. The influenza virus output files have the wildcard set

{center}_{lineage}_{segment}_{resolution}_{passage}_{assay}

that currently use the following values:

• center: [who, cdc, crick, niid, vidrl]
• lineage: [h3n2, h1n1pdm, vic, yam]
• segment: [ha, na]
• resolution: [6m, 2y, 3y, 6y, 12y]
• assay: [hi, fra]
• passage: [cell, egg]

Intermediate files follow this wildcard ordering, but may omit irrelevant wildcards, eg filtered_h3n2_ha.fasta.

To manage both builds for the general public and the different WHO collaborating centers, the Snakefiles are split into a Snakefile_base that contains the rules for the core analysis and the files, alongside:

• Snakefile for the standard "live" build housed at nextstrain.org/flu
• Snakefile_WHO for the WHO CC builds
• Snakefile_report to generate figures and additional analysis for the biannual reports to the WHO

The latter Snakefiles import the rules specified in Snakefile_base, define additional rules, and specify the build targets.

fauna / RethinkDB credentials

This build starts by pulling sequences from our live fauna database (a RethinkDB instance). This requires environment variables RETHINK_HOST and RETHINK_AUTH_KEY to be set.

If you don't have access to our database, you can run the build using the example data provided in this repository. Before running the build, copy the example sequences into the data/ directory like so:

mkdir data/
cp example_data/* data/

Then run the the build via:

nextstrain build . targets/flu_seasonal_h3n2_ha_12y