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nextclade

List of commands for nextclade:

  • nextclade:tldr:33d3d nextclade: Try reverse complement if sequence does not align.
    $ nextclade run --retry-reverse-complement -d ${dataset_name} -t ${path-to-output_tsv} ${path-to-input_fasta}
    try on your machine
    explain this command
  • nextclade:tldr:4f277 nextclade: Use a downloaded [D]ataset, producing all [O]utputs.
    $ nextclade run -D ${path-to-dataset_dir} -O ${path-to-output_dir} ${path-to-dataset_dir-sequences-fasta}
    try on your machine
    explain this command
  • nextclade:tldr:53055 nextclade: List all available datasets.
    $ nextclade dataset list
    try on your machine
    explain this command
  • nextclade:tldr:7464c nextclade: Download the latest SARS-CoV-2 dataset.
    $ nextclade dataset get --name sars-cov-2 --output-dir ${path-to-directory}
    try on your machine
    explain this command
  • nextclade:tldr:cfe7d nextclade: Create a TSV report, auto-downloading the latest [d]ataset.
    $ nextclade run -d ${dataset_name} ${path-to-fasta} -t ${path-to-output_tsv}
    try on your machine
    explain this command
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