From be8233b8bb57f309186bfe4dd827a858faa9ff81 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Fri, 26 Aug 2022 22:25:21 +0200 Subject: [PATCH] nextclade: add page (#8400) --- pages/common/nextclade.md | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 pages/common/nextclade.md diff --git a/pages/common/nextclade.md b/pages/common/nextclade.md new file mode 100644 index 0000000000..cca28e9699 --- /dev/null +++ b/pages/common/nextclade.md @@ -0,0 +1,28 @@ +# nextclade + +> Bioinformatics tool for virus genome alignment, clade assignment and qc checks. +> More information: . + +- Create a TSV report, auto-downloading the latest [d]ataset: + +`nextclade run -d {{dataset_name}} {{path/to/fasta}} -t {{path/to/output_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/dataset_dir/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}}`