nextclade:tldr:33d3d

nextclade: Try reverse complement if sequence does not align.

nextclade

$ nextclade run --retry-reverse-complement -d ${dataset_name} -t ${path-to-output_tsv} ${path-to-input_fasta}

try on your machine

The command nextclade run is used to run the Nextclade tool, which is a software program used for analyzing viral genome sequences.

Here is a breakdown of the command:

--retry-reverse-complement: This is an option/flag used with the nextclade run command. It specifies that if the provided input sequence is not in the correct orientation (reverse complement), Nextclade should automatically try the reverse complement and analyze it.
-d ${dataset_name}: This option/flag specifies the name of the dataset to be used by Nextclade. The value ${dataset_name} is a placeholder that should be replaced with the actual name of the dataset.
-t ${path-to-output_tsv}: This option/flag specifies the path to the output TSV file that will be generated by Nextclade. The value ${path-to-output_tsv} is a placeholder that should be replaced with the actual path to the desired output TSV file.
${path-to-input_fasta}: This is the path to the input FASTA file containing the viral genome sequence that you want to analyze. It is a placeholder that should be replaced with the actual path to the input FASTA file.

Overall, this command runs Nextclade with the specified options/flags, dataset, and input file, and generates an output TSV file containing the analysis results.

This explanation was created by an AI. In most cases those are correct. But please always be careful and never run a command you are not sure if it is safe.

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