snipe pangenome

Pangenome analysis: identify core and accessory k-mers across samples.

snipe pangenome [OPTIONS]

Options

Flag	Type	Required	Default	Description
-o, --output-prefix	text	yes	—	Output prefix for generated files.
-i, --input	text	no	—	Input .snipesig signature files (repeat the flag per file; mutually exclusive with —input-list).
-l, --input-list	text	no	—	File containing paths to signature files, one per line.
--out-sourmash	flag	no	off	Also emit a sourmash .sig alongside the .snipesig.
--filter-singleton-errors	flag	no	off	Filter singleton errors (abundance=1 in the original sample).
--min-samples	integer	no	—	Minimum number of samples a hash must appear in.
--min-percent	float	no	—	Minimum percentage of samples a hash must appear in (0-100).
--max-samples	integer	no	—	Maximum number of samples a hash can appear in.
--max-percent	float	no	—	Maximum percentage of samples a hash can appear in (0-100).
--genome	text	no	—	Optional reference genome for comparison.
-s, --stats	flag	no	off	Output detailed statistics.
--export-distribution	flag	no	off	Export the hash prevalence distribution as a TSV.
--allow-duplicate-inputs	flag	no	off	Allow the same input file to appear more than once.