wa_sc2

WA-focused ncov Nexstrain builds for genomic surveillance of SARS-CoV-2 in Washington state. Builds located here:

• Washington-focused SARS-CoV-2 genomic analysis: Past two months
• Washington-focused SARS-CoV-2 genomic analysis: Past four months
• Washington-focused SARS-CoV-2 genomic analysis: Past six months

Setup

First, install the ncov nextstrain pipeline and clone the ncov repository using git clone https://github.com/nextstrain/ncov or gh repo clone nextstrain/ncov.

Next, clone this repository in the ncov folder. You can do this in the command-line terminal by navigating to the ncov repository using cd ncov and then cloning the repository using git clone https://github.com/DOH-SML1303/wa_sc2.git or gh repo clone DOH-SML1303/wa_sc2.

County-level metadata file

The WA-Focused build includes county level metadata for the sequences that may not be present in Genbank. For Molecular Epi folks, this data can be retrieved from the Y-drive. When you retrieve this file, change the file name to county_metadata.csv and move it into the wa_data/ folder prior to running the fetch_n_process.smk workflow.

Retrieving sequencing and metadata files for the WA-focused ncov nextstrain

The SARS-CoV-2 datasets are maintained by the Nextstrain team. You can view the list of remote datasets here.

A workflow has been configured for you to pull the inputs that you will need for the WA-focused build. To run this workflow, first cd wa_sc2 to navigate to the wa_sc2 repository. Next, to run the workflow, run snakemake -s wa_workflow/fetch_n_process.smk --cores 6. You can specify different number of cores to use for the workflow based on your computing capacity.

Configuring the WA-focused build

Prior to running the WA-focused build, you will need to update your input locations in the wa_sc2/wa_profiles/wa-subsampled-background-genbank/subsampled-background-builds.yaml on lines 13 to 20. The subsampled-background-builds.yaml is set up for you to move your data into an S3 Bucket, but you can keep the files locally. If you decide to move the data to an S3 bucket the recommended path would be s3://bucket-name/ncov/data/wa-sequences.tar.xz" for both the metadata and sequencing data inputs.

If you decide to keep things locally then the file path might look something like this: wa_sc2/wa_data/wa-sequences.tar.xz

Running the builds

This ncov Nexstrain build sources data from Genbank and inclues a 2m, 4m, and 6m build. Once you have your inputs and have updated the subsampled-background-builds.yaml with the input location, you can run the pipeline. If you're running Nextstrain in a conda environment then you want to make sure you pull the latest ncov github repository updates first by running git pull in the ncov directory, activating the conda environment using conda activate nextstrain followed by nextstrain update to update Nextstrain. It's recommended to pull updates prior to running the pipeline. The same could also be said for this repo as well! :)

To run the builds using inputs stored on an AWS Bucket:

You can configure your AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY in your AWS credentials file which can be accessed in terminal using nano ~/.aws/credentials, or you can simply export the environmental variables upon opening a terminal window using: export AWS_ACCESS_KEY_ID= export AWS_SECRET_ACCESS_KEY=

If you're running Batch then you need to make sure all of the information is included in your ~/.nextstrain/config. File. See this documentation for more information.

To run the builds with your data stored in an AWS Bucket, navigate to the ncov directory and run: nextstrain build --aws-batch-s3-bucket bucket-name --cpus=6 . --profile wa_sc2/wa_profiles/wa-subsampled-background-genbank

Run the builds locally

nextstrain build --cpus=6 . --profile wa_sc2/wa_profiles/wa-subsampled-background-genbank

Visualizing the results

You can check your results once the pipeline is done running using nextstrain view auspice