nextclade

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

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]