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
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.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
Last modified 1yr ago