Previous versions of nextclade had the data (a reference tree, reference sequence, and configs) bundled into the javascript/node bundle.
Nextclade 1.* is written in C++ and doesn’t bundle these data. Those used as default by the nextclade web app can be found here
Please download those (possibly via curl
or wget
). These are passed into nextclade
as follows
nextclade -i my_sequences.fasta \
--input-root-seq reference.fasta \
--input-tree tree.json \
--input-gene-map genemap.gff \
--input-qc-config qc.json \
--output-tsv nextclade_results.tsv
--output-dir alignments
--jobs 16
There are multiple other output files that can be specified via analogous flags,
You can find the latest releases here:
See nextclade --help
for more details!