This workflow automates the comparison of your genomes, Metagenome-Assembled Genomes (MAGs), or Single-Cell Amplified Genomes (SAGs) against a reference project for taxonomy.

A reference project has to be a separate MiGA project with a database of your choice, taxonomically annotated, and fully indexed. If you want to use the pre-processed database provided by MiGA Online, run:

miga download

To execute the workflow, run:

miga classify_wf -o my_project path/to/mags/*.fasta

For additional options, run:

miga classify_wf -h

Expected output

Once your run is complete, you may expect the standard summaries for cds, assembly, essential_genes, and taxonomy, as well as a summary classification table (classification.tsv) with two columns: (1) the genome name, and (2) the space-delimited classification of the genome with taxon names prefixed by the rank code and a colon. Something like:

NZ_CP010409_1    d:Bacteria p:Proteobacteria c:Gammaproteobacteria o:Xanthomonadales f:Xanthomonadaceae g:Xanthomonas s:Xanthomonas_sacchari
NZ_CP016878_1    d:Bacteria p:Proteobacteria c:Gammaproteobacteria o:Xanthomonadales f:Xanthomonadaceae g:Xanthomonas s:Xanthomonas_hortoru
[...]