CmdID

CmdID / Commands

nextclade

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

On several platforms

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Several platforms

from tldr-pages, CC BY 4.0

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

nextclade run path/to/sequences.fa --input-ref path/to/reference.fa --output-fasta path/to/alignment.faIdentify

Create a TSV report, auto-downloading the latest dataset

nextclade run path/to/fasta --dataset-name dataset_name --output-tsv path/to/report.tsvIdentify

List all available datasets

nextclade dataset listIdentify

Download the latest SARS-CoV-2 dataset

nextclade dataset get --name sars-cov-2 --output-dir path/to/directoryIdentify

Use a downloaded dataset, producing all outputs

nextclade run --input-dataset path/to/dataset_directory --output-all path/to/output_directory path/to/sequences.fastaIdentify

Run on multiple files

nextclade run --dataset-name dataset_name --output-tsv path/to/output_tsv -- path/to/input_fasta_1 path/to/input_fasta_2 ...Identify

Try reverse complement if sequence does not align

nextclade run --retry-reverse-complement --dataset-name dataset_name --output-tsv path/to/output_tsv path/to/input_fastaIdentify