CLI reference

Aviary exposes eight subcommands. The installed command's --help output is the final authority for the installed version.

Start with command syntax for global-option placement, boolean values, list inputs, aliases and quoting rules.

Command	Purpose
assemble	Quality-control reads and assemble contigs
recover	Recover and assess MAGs from an assembly
annotate	Annotate a directory of genome FASTA files
complete	Run the applicable metagenome stages end to end
cluster	Dereplicate genomes across completed runs
isolate	Assemble reads from a cultured isolate
configure	Store reference-data paths and request downloads
build	Build dependency environments; add --gpu for GPU environments

Shared workflow and resource options are explained in shared options.