nextclade

all

Bioinformatics tool for virus genome alignment, clade assignment and qc checks.

Options (8)

-r, --input-refboolean

Align sequences to user provided reference, outputting the alignment to a file

Example:

nextclade run {{path/to/sequences.fa}} {{[-r|--input-ref]}} {{path/to/reference.fa}} {{[-o|--output-fasta]}} {{path/to/alignment.fa}}

-o, --output-fastaboolean

Align sequences to user provided reference, outputting the alignment to a file

Example:

nextclade run {{path/to/sequences.fa}} {{[-r|--input-ref]}} {{path/to/reference.fa}} {{[-o|--output-fasta]}} {{path/to/alignment.fa}}

-d, --dataset-nameboolean

Create a TSV report, auto-downloading the latest dataset

Example: nextclade run {{path/to/fasta}} {{[-d|--dataset-name]}} {{dataset_name}} {{[-t|--output-tsv]}} {{path/to/report.tsv}}

-t, --output-tsvboolean

Create a TSV report, auto-downloading the latest dataset

Example: nextclade run {{path/to/fasta}} {{[-d|--dataset-name]}} {{dataset_name}} {{[-t|--output-tsv]}} {{path/to/report.tsv}}

-n, --nameboolean

Download the latest SARS-CoV-2 dataset

Example: nextclade dataset get {{[-n|--name]}} sars-cov-2 {{[-o|--output-dir]}} {{path/to/directory}}

-o, --output-dirboolean

Download the latest SARS-CoV-2 dataset

Example: nextclade dataset get {{[-n|--name]}} sars-cov-2 {{[-o|--output-dir]}} {{path/to/directory}}

-D, --input-datasetboolean

Use a downloaded dataset, producing all outputs

Example:

nextclade run {{[-D|--input-dataset]}} {{path/to/dataset_directory}} {{[-O|--output-all]}} {{path/to/output_directory}} {{path/to/sequences.fasta}}

-O, --output-allboolean

Use a downloaded dataset, producing all outputs

Example:

nextclade run {{[-D|--input-dataset]}} {{path/to/dataset_directory}} {{[-O|--output-all]}} {{path/to/output_directory}} {{path/to/sequences.fasta}}

Align sequences to user provided reference, outputting the alignment to a file

nextclade run path/to/sequences.fa [-r|--input-ref] path/to/reference.fa [-o|--output-fasta] path/to/alignment.fa

Create a TSV report, auto-downloading the latest dataset

nextclade run path/to/fasta [-d|--dataset-name] dataset_name [-t|--output-tsv] path/to/report.tsv

List all available datasets

nextclade dataset list

Download the latest SARS-CoV-2 dataset

nextclade dataset get [-n|--name] sars-cov-2 [-o|--output-dir] path/to/directory

Use a downloaded dataset, producing all outputs

nextclade run [-D|--input-dataset] path/to/dataset_directory [-O|--output-all] path/to/output_directory path/to/sequences.fasta

Run on multiple files

nextclade run [-d|--dataset-name] dataset_name [-t|--output-tsv] 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] dataset_name [-t|--output-tsv] path/to/output_tsv path/to/input_fasta