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nextclade: add alignment example (#12212)

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* nextclade: add alignment example

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Co-authored-by: Vitor Henrique <87824454+vitorhcl@users.noreply.github.com>
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Cornelius Roemer 2024-02-19 17:36:25 +01:00 • committed by GitHub
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@ -1,11 +1,15 @@
# nextclade # nextclade
> Bioinformatics tool for virus genome alignment, clade assignment and qc checks. > 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>. > More information: <https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-cli/index.html>.
- Create a TSV report, auto-downloading the latest [d]ataset: - Align sequences to user provided [r]eference, [o]utputting the alignment to a file:
`nextclade run -d {{dataset_name}} {{path/to/fasta}} -t {{path/to/output_tsv}}` `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: - List all available datasets:
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- Use a downloaded [D]ataset, producing all [O]utputs: - 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}}` `nextclade run -D {{path/to/dataset_dir}} -O {{path/to/output_dir}} {{path/to/sequences.fasta}}`
- Run on multiple files: - Run on multiple files: