nextclade

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

TLDR

Create a TSV report, auto-downloading the latest [d]ataset

$ nextclade run -d [dataset_name] [path/to/fasta] -t [path/to/output_tsv]
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List all available datasets
$ nextclade dataset list
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Download the latest SARS-CoV-2 dataset
$ 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
$ nextclade run -D [path/to/dataset_dir] -O [path/to/output_dir] [path/to/dataset_dir/sequences.fasta]
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Run on multiple files
$ 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
$ nextclade run --retry-reverse-complement -d [dataset_name] -t [path/to/output_tsv] [path/to/input_fasta]
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