Nextstrain build pipeline for the WestNile 4K Project
This is the repository used to build nextstrain.org/WNV/NA
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To automatically download all WNV data (genomes and metadata) from NCBI, run the following command. This will generate the basic inputs to run the analysis.
python download_sequences.py --mode separate
This will get all genome sequences and associated metadata from NCBI.
If existing files are provided (see examples inside input_files folder above), the command below will avoid re-downloading entries already present in the files (genomes and rows of metadata), and will resume the download of new entries, only.
python download_sequences.py --sequences sequences.fasta --metadata metadata.tsv --mode append
The argument --append above will append the newly downloaded sequences and metadata rows at the bottom of the corresponding files. If --separate is used, separate files will be generated. If names for --output1 and --output2 are provided, those will be the names of the newly generated FASTA file and metadata, respectively.
Run the command below to see more instructions:
python download_sequences.py --h
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