This is the Nextstrain build for chikunguny virus (CHIKV).
Input metadata and sequences will be made available via https://data.nextstrain.org
These data are generously shared by labs around the world and deposited in NCBI genbank by the authors.
Please contact these labs first if you plan to publish using these data.
CHIKV sequences and metadata can be downloaded in the /ingest folder using
nextstrain build --cpus 1 ingest or nextstrain build --cpus 1 . if running directly from the /ingest directory.
Running the ingest pipeline produces ingest/data/metadata.tsv, ingest/data/extended_metadata.tsv and "ingest/data/sequences.fasta".
-- change metadata name (extended)
Once you have run the ingest pipeline locally you can copy the files into the top-level data directory so that the main phylo workflow uses these files rather than downloading from s3:
mkdir -p data
for i in ingest/data/*/{metadata.tsv,sequences.fasta}; do cp $i ${i#ingest/}; doneThis repository uses git subrepo to manage copies of ingest scripts in ingest/vendored, from nextstrain/ingest. To pull new changes from the central ingest repository, first install git subrepo, then run:
See ingest/vendored/README.md for instructions on how to update the vendored scripts.
The workflow produces whole genome and G gene trees for RSV-A and RSV-B.
To run the workflow, use snakemake -j4 -p --configfile config/configfile.yaml and nextstrain view auspice to visualise results.
Follow the standard installation instructions for Nextstrain's suite of software tools.
We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances.