From 8963602e7f3a0c4731d18adab375e82e5072586b Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Mon, 19 Feb 2024 17:36:25 +0100 Subject: [PATCH] nextclade: add alignment example (#12212) * nextclade: add alignment example --------- Co-authored-by: Vitor Henrique <87824454+vitorhcl@users.noreply.github.com> --- pages/common/nextclade.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/pages/common/nextclade.md b/pages/common/nextclade.md index cca28e969..dec5bbf8d 100644 --- a/pages/common/nextclade.md +++ b/pages/common/nextclade.md @@ -1,11 +1,15 @@ # nextclade > Bioinformatics tool for virus genome alignment, clade assignment and qc checks. -> More information: . +> More information: . -- Create a TSV report, auto-downloading the latest [d]ataset: +- Align sequences to user provided [r]eference, [o]utputting the alignment to a file: -`nextclade run -d {{dataset_name}} {{path/to/fasta}} -t {{path/to/output_tsv}}` +`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: @@ -17,7 +21,7 @@ - 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}}` +`nextclade run -D {{path/to/dataset_dir}} -O {{path/to/output_dir}} {{path/to/sequences.fasta}}` - Run on multiple files: