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* nextclade: add alignment example --------- Co-authored-by: Vitor Henrique <87824454+vitorhcl@users.noreply.github.com>
32 lines
1.2 KiB
Markdown
32 lines
1.2 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/index.html>.
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- Align sequences to user provided [r]eference, [o]utputting the alignment to a file:
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`nextclade run {{path/to/sequences.fa}} -r {{path/to/reference.fa}} -o {{path/to/alignment.fa}}`
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- Create a [t]SV report, auto-downloading the latest [d]ataset:
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`nextclade run {{path/to/fasta}} -d {{dataset_name}} -t {{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 --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/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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