nextclade
Verified for current stable LTS
Nextclade Commands
Nextclade command syntax with verified terminal examples.
Commands
7 commands for Nextclade
nextclade Operations
Nextclade Command: Align Sequences To Reference Output Alignment
nextclade run <path/to/sequences.fa> -r <path/to/reference.fa> -o <path/to/alignment.fa> nextclade HTTP
Nextclade Command: Create Tsv Report Auto Download Dataset
nextclade run <path/to/fasta> -d <dataset_name> -t <path/to/report.tsv> nextclade HTTP
Nextclade Command: Download Latest Sars Cov 2 Dataset
nextclade dataset get -n sars-cov-2 -o <path/to/directory> nextclade Operations
Nextclade Command: List Available Datasets
nextclade dataset list nextclade Operations
Nextclade Command: Run On Multiple Files
nextclade run -d <dataset_name> -t <path/to/output_tsv> -- <path/to/input_fasta_1 path/to/input_fasta_2 ...> nextclade Operations
Nextclade Command: Try Reverse Complement If Sequence Not Align
nextclade run --retry-reverse-complement -d <dataset_name> -t <path/to/output_tsv> <path/to/input_fasta> nextclade HTTP
Nextclade Command: Use Downloaded Dataset Produce All Outputs
nextclade run -D <path/to/dataset_directory> -O <path/to/output_directory> <path/to/sequences.fasta> Suggest a Nextclade Command
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FAQ
Coverage: Focused examples for common Nextclade workflows.
Verified version: current stable LTS.
Verification: Test commands in a disposable workspace and submit notes for edge cases.