nextclade

Bioinformatics tool for virus genome alignment, clade assignment and qc checks. More information: https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-cli.html.

• Create a TSV report, auto-downloading the latest [d]ataset:
  nextclade run -d {{dataset_name}} {{path/to/fasta}} -t {{path/to/output_tsv}}
• List all available datasets:
  nextclade dataset list
• Download the latest SARS-CoV-2 dataset:
  nextclade dataset get --name sars-cov-2 --output-dir {{path/to/directory}}
• 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}}
• Run on multiple files:
  nextclade run -d {{dataset_name}} -t {{path/to/output_tsv}} -- {{path/to/input_fasta_1 path/to/input_fasta_2 ...}}
• 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}}