lilith/tldr
1
0
Fork 0
mirror of https://github.com/tldr-pages/tldr.git synced 2025-04-22 01:22:09 +02:00
Code Activity

nextclade: add alignment example (#12212)

Browse source 
* nextclade: add alignment example

---------

Co-authored-by: Vitor Henrique <87824454+vitorhcl@users.noreply.github.com>
This commit is contained in:
Cornelius Roemer 2024-02-19 17:36:25 +01:00 • committed by GitHub
parent 13ebe1e3cf
commit 8963602e7f
No known key found for this signature in database
GPG key ID: B5690EEEBB952194
1 changed files with 8 additions and 4 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

12
pages/common/nextclade.md
View file

@ -1,11 +1,15 @@
# 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.html>.
> More information: <https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-cli/index.html>.
- 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: