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+# 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}}`