This repo contains build files for the SPHERES builds hosted by the Nextstrain and a description the upstream subsampling steps performed prior to the analysis pipeline.
The previous version of this repo can be found in the archive branch
Clone this repository.
git clone https://github.com/CDCgov/spheres-augur-build.git
cd spheres-augur-build/Select the appropriate build in the spheres_profile directory and copy it's contents to a directory named build in your ncov directory.
Modify build definitions, as needed, in builds.yaml and config.yaml files.
By default, each build requires specificly named data files to be placed in the ncov/data directory
"references" data
Files: data/references_sequences.fasta and data/references_metadata.tsv
Description: Sequence and metadata for Wuhan reference sequences. Provided with Nextstrain ncov repository
"global_background" data
Files: data/global_background.fasta and data/global_background.tsv
Description: Sequence and metadata for non-USA background sequences. User must provide these files.
"usa" data
Files: data/usa_background.fasta and data/usa_background.tsv
Description: Sequence and metadata for USA background sequences. User must provide these files.
"focus" data
Files: data/<BUILD_NAME>.fasta and data/<BUILD NAME>.tsv
Description: Sequence and metadata for focus division. User must provide these files.
Run the workflow.
snakemake --profile build/View the resulting builds through auspice.us or with auspice installed on your local machine.
auspice viewThe Nextstrain team constantly improves the ncov workflow. We recommend that you regularly update your ncov workflow to take advantage of new feature additions. This repo is no longer dependent on a specific ncov distribution, so these build files are compatible with Docker based workflows and can be updated independently of the ncov workflow.
The build files hosted in this repo are used to generate the publicly hosted SPHERES builds, however most of the subsampling operations take place upstream of the Nextstrain ncov workflow. This allows for improved run-time performance and greater portability. This section describes the subsampling used to produce the SPHERES builds. All input data files described here are oversampled relative to the requirements in the build file to provide some flexibility in downstream subsampling by the Nextstrain augur pipeline.
All included data is prepared using these rules prior to any subsampling operations
- Sequence and metadata is derived from Sars-CoV-2 sequence data provided by the GISAID Initiative
- In the case of duplicated accession numbers (EPI_ISL_), only the most recently submitted version is retained
- Additional metadata is added from the Nextstrain curation
- Sequence length must exceed 27000 base pairs
- Sequences are selected randomly from all sequences matching the sampling criteria
- If an insufficient number of sequences are available for a given subsampling target, that data partition will contain all available sequences meeting that criteria
This data provides global context to the USA sequences. The global_background files are shared between all builds on a given week, but is re-calculated each week.
- 25 sequences collected within the last two months from each global region ("Africa" "Asia" "Europe" "North America" "Oceania" "South America" )
- 25 sequences collected prior to last two months from each global region ("Africa" "Asia" "Europe" "North America" "Oceania" "South America" )
This data is provides USA context to the focal sequences. The usa_background files are shared between all builds on a given week, but is re-calculated each week
- 10 sequences collected within the last two months from each of the included states, unincorporated territory of the United States, and Palau
- 10 sequences collected prior to last two months from each of the included states, unincorporated territory of the United States, and Palau
This data is densely sampled focal data of the build. These data files are specific to each build and are not shared with other builds.
- 1000 sequences collected within the last two months from the focal division
- 1000 sequences collected prior to last two months from the focal division
This data provides an overview of circulating and historical sequences in the United States, unincorporated territory of the United States, and Palau. These files are used for the "usa" build only
- 25 sequences collected within the last two months from each of the included states, unincorporated territory of the United States, and Palau
- 25 sequences collected prior to last two months from each of the included states, unincorporated territory of the United States, and Palau
This data provides an overview of circulating and historical sequences in the United States and unincorporated territory of the United States generated by the NS3 project. These files are used for the "ns3" build only
- 25 sequences collected as part of the NS3 project within the last two months from each of the included states, unincorporated territory of the United States, and Palau
- 25 sequences collected as part of the NS3 project prior to last two months from each of the included states, unincorporated territory of the United States, and Palau
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