Table:)

ganon table filters and summarizes several reports obtained with ganon report into a table. Filters for each sample or for averages among all samples can also be applied.

Examples:)

Given several .tre from ganon report:

Counts of species:)

ganon table --input *.tre --output-file table.tsv --rank species

Abundance of species:)

ganon table --input *.tre --output-file table.tsv --output-value percentage --rank species

Top 10 species (among all samples):)

ganon table --input *.tre --output-file table.tsv --output-value percentage --rank species --top-all 10

Top 10 species (from each samples):)

ganon table --input *.tre --output-file table.tsv --output-value percentage --rank species --top-sample 10

Filtering results:)

ganon table --input *.tre --output-file table.tsv --output-value percentage --rank species --min-count 0.0005

This will keep only results with a min. abundance of 0.05%.