Migrating from nextclade 0.* to 1.* for CLI use

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!