Index
Last updated
Last updated
This workflow automates the indexing of your genomic collection.
To execute the workflow, run:
For additional options, run:
Once your run is complete, you may expect the 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 .
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: