phylogenetic

nextstrain.org/dengue

This is the Nextstrain build for dengue. Output from this build is visible at nextstrain.org/dengue.

Software requirements

Follow the standard installation instructions for Nextstrain's suite of software tools.

Usage

If you're unfamiliar with Nextstrain builds, you may want to follow our Running a Pathogen Workflow guide first and then come back here.

The easiest way to run this pathogen build is using the Nextstrain command-line tool:

nextstrain build .

Build output goes into the directories data/, results/ and auspice/.

Once you've run the build, you can view the results in auspice:

nextstrain view auspice/

Configuration

Configuration for the workflow takes place entirely within the defaults/config_dengue.ymal. The analysis pipeline is contained in Snakefile with included rules. Each rule specifies its file inputs and output and pulls its parameters from the config. There is little redirection and each rule should be able to be reasoned with on its own.

The config that was used during the run of the workflow is output to results/run_config.yaml.

Default input data

The default builds start from the public Nextstrain data that have been preprocessed and cleaned from NCBI GenBank.

serotypes: ['all', 'denv1', 'denv2', 'denv3', 'denv4']
inputs:
  - name: ncbi
    metadata: "https://data.nextstrain.org/files/workflows/dengue/metadata_{serotype}.tsv.zst"
    sequences: "https://data.nextstrain.org/files/workflows/dengue/sequences_{serotype}.fasta.zst"

Note the inputs require the {serotype} expandable field, to be replaced by the config parameter serotypes values.

Adding your own data

If you want to add your own data to the default input, specify your inputs with the additional_inputs config parameter. For example, this repo has a small set of example data that could be added to the default inputs via:

additional_inputs:
  - name: example-data
    metadata: example_data/metadata_{serotype}.tsv
    sequences: example_data/sequences_{serotype}.fasta

Note that the additional inputs also require the {serotype} expandable field. If you only have data for a single serotype, e.g. denv1, then you can do so with

serotypes: ["denv1"]
additional_inputs:
  - name: private
    metadata: private/metadata_{serotype}.tsv
    sequences: private/sequences_{serotype}.fasta

If you want to run the builds without the default data and only use your own data, you can do so by specifying the inputs parameter.

inputs:
  - name: example-data
    metadata: example_data/metadata_{serotype}.tsv
    sequences: example_data/sequences_{serotype}.fasta

Using example data

Alternatively, 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:

nextstrain build .  --configfile profiles/ci/profiles_config.yaml

AWS

With access to AWS, this can be more quickly run as:

nextstrain build --aws-batch --aws-batch-cpus 4 --aws-batch-memory 7200 . --jobs 4

Deploying build

To run the workflow and automatically deploy the build to nextstrain.org, you will need to have AWS credentials to run the following:

nextstrain build \
    --env AWS_ACCESS_KEY_ID \
    --env AWS_SECRET_ACCESS_KEY \
    . \
        deploy_all \
        --configfile build-configs/nextstrain-automation/config.yaml