FAQ.md

Frequently Asked Questions

1. Is it required to run leviathan-profile-taxonomy before leviathan-profile-pathway or vice versa?

No, they are functionally independent. However, you can always filter the pathway profiling results by taxonomic filters post hoc.

# Load taxonomic profiling
ds_taxonomic = xr.open_dataset("leviathan_output/artifacts/taxonomic_abundances.genome_clusters.nc")

# Load functional profiling
ds_pathway = xr.open_dataset("leviathan_output/artifacts/pathway.genome_clusters.nc")

# Get (pan)genomes to retain from taxonomic abundances
minimum_samples_detected = 2
retained_organisms = (ds_taxonomic["taxonomic_abundances"].to_pandas() > 0).sum(axis=0)[lambda x: x >= minimum_samples_detected].index

# Filter functional profiling with taxonomic abundance gate
ds_pathway_filtered = ds_pathway.sel(genome_clusters=retained_organisms)

2. How can I estimate the reference coverage (i.e., percent of assigned reads)?

# Load taxonomic profiling
ds_taxonomic = xr.open_dataset("leviathan_output/artifacts/taxonomic_abundances.genome_clusters.nc")

# Sum the sequence abundances (not taxonomic abundances)
percent_assigned_reads = ds_taxonomic["sequence_abundances"].sum(axis=1).to_pandas()
percent_unassigned_reads = 100 - percent_assigned_reads

3. Do I need my own genomes or are there reference catalogs?