mirror of https://github.com/CrimsonTome/tldr.git
29 lines
1000 B
Markdown
29 lines
1000 B
Markdown
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# 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.html>.
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- Create a TSV report, auto-downloading the latest [d]ataset:
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`nextclade run -d {{dataset_name}} {{path/to/fasta}} -t {{path/to/output_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 --name sars-cov-2 --output-dir {{path/to/directory}}`
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- Use a downloaded [D]ataset, producing all [O]utputs:
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`nextclade run -D {{path/to/dataset_dir}} -O {{path/to/output_dir}} {{path/to/dataset_dir/sequences.fasta}}`
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- Run on multiple files:
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`nextclade run -d {{dataset_name}} -t {{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}} -t {{path/to/output_tsv}} {{path/to/input_fasta}}`
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