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/reference.html.

• 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_dir}} {{[-O|--output-all]}} {{path/to/output_dir}} {{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}}