nextclade

Bioinformatics tool for virus genome alignment, clade assignment and qc checks. More information: https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-cli/index.html.

• Align sequences to user provided [r]eference, [o]utputting the alignment to a file:

nextclade run path/to/sequences.fa -r path/to/reference.fa -o path/to/alignment.fa

• Create a [t]SV report, auto-downloading the latest [d]ataset:

nextclade run path/to/fasta -d dataset_name -t path/to/report.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/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