Classify
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:
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miga download
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To execute the workflow, run:
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miga classify_wf -o my_project path/to/mags/*.fasta
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For additional options, run:
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miga classify_wf -h
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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:1
NZ_CP010409_1 d:Bacteria p:Proteobacteria c:Gammaproteobacteria o:Xanthomonadales f:Xanthomonadaceae g:Xanthomonas s:Xanthomonas_sacchari
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NZ_CP016878_1 d:Bacteria p:Proteobacteria c:Gammaproteobacteria o:Xanthomonadales f:Xanthomonadaceae g:Xanthomonas s:Xanthomonas_hortoru
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[...]
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Last modified 1yr ago
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Contents
Expected output