Index

This workflow automates the indexing of your genomic collection.

To execute the workflow, run:

miga index_wf -o my_project path/to/genomes/*.fasta

For additional options, run:

miga index_wf -h

Expected output

Once your run is complete, you may expect the standard summaries for cds, assembly, essential_genes, and ssu. Additionally all the intermediate files are preserved, including assemblies, predicted genes, and detected essential and ribosomal genes. Importantly, all-vs-all comparisons are generated using Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), making this a queriable project.

Indexing publicly available genomes

It is also possible to use this workflow on genomes publicly available in NCBI. This enables taxonomic analysis, such as using this indexed project as a reference database for the classification workflow.

For example, to download and index all the genomes from the species Xanthomonas vesicatoria using Diamond for AAI and FastANI for ANI estimation (--fast flag), run:

miga index_wf -o X_vesicatoria \
  -T 'Xanthomonas vesicatoria' --project-type clade --fast -v