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32 lines
1.4 KiB
Markdown
32 lines
1.4 KiB
Markdown
# nextclade
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> Bioinformatics tool for virus genome alignment, clade assignment and qc checks.
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> More information: <https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-cli/reference.html>.
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- Align sequences to user provided reference, outputting the alignment to a file:
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`nextclade run {{path/to/sequences.fa}} {{[-r|--input-ref]}} {{path/to/reference.fa}} {{[-o|--output-fasta]}} {{path/to/alignment.fa}}`
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- Create a TSV report, auto-downloading the latest dataset:
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`nextclade run {{path/to/fasta}} {{[-d|--dataset-name]}} {{dataset_name}} {{[-t|--output-tsv]}} {{path/to/report.tsv}}`
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- List all available datasets:
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`nextclade dataset list`
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- Download the latest SARS-CoV-2 dataset:
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`nextclade dataset get {{[-n|--name]}} sars-cov-2 {{[-o|--output-dir]}} {{path/to/directory}}`
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- Use a downloaded dataset, producing all outputs:
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`nextclade run {{[-D|--input-dataset]}} {{path/to/dataset_dir}} {{[-O|--output-all]}} {{path/to/output_dir}} {{path/to/sequences.fasta}}`
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- Run on multiple files:
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`nextclade run {{[-d|--dataset-name]}} {{dataset_name}} {{[-t|--output-tsv]}} {{path/to/output_tsv}} -- {{path/to/input_fasta_1 path/to/input_fasta_2 ...}}`
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- Try reverse complement if sequence does not align:
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`nextclade run --retry-reverse-complement {{[-d|--dataset-name]}} {{dataset_name}} {{[-t|--output-tsv]}} {{path/to/output_tsv}} {{path/to/input_fasta}}`
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