tldr/pages/common/nextclade.md

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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/index.html>.
- Align sequences to user provided [r]eference, [o]utputting the alignment to a file:
`nextclade run {{path/to/sequences.fa}} -r {{path/to/reference.fa}} -o {{path/to/alignment.fa}}`
- Create a [t]SV report, auto-downloading the latest [d]ataset:
`nextclade run {{path/to/fasta}} -d {{dataset_name}} -t {{path/to/report.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/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}}`