Installation

Architeuthis is a standalone binary. Some of its installation requires taxonkit I recommend you install this as well (already done when using conda).

Conda or Mamba

architeuthis is provided within bioconda and can be installed via

conda install -c conda-forge -c bioconda architeuthis

Binary release

You can also simply download a binary for your system from the releases page. Either execute it in the containing folder order add it to your $PATH.

Choose a NCBI Taxonomy version

This will also install taxonkit. If you want to use a new or custom version of the NCBI taxonomy you need to set that up with taxonkit.

In case you have built your own Kraken database it is also possible to use the taxonomy directly from there. For this simply add the --db option to your architeuthis calls. For instance:

architeuthis --db /path/to/my/kraken_db lineage my_file.b2

Which Taxonomy to use?

Unless you specifically want to reclassify under a different taxonomy, I recommend to always use the taxonomy from the Kraken DB if available.