mirror of
https://github.com/tldr-pages/tldr.git
synced 2025-04-23 14:02:08 +02:00
28 lines
1,000 B
Markdown
28 lines
1,000 B
Markdown
# 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}}`
|