Synopsis:

Combine multiple Snippy folders into a core SNP alignment

Usage:

../../snippy/bin/snippy-core [options] [--noref] snippyDir1/ snippyDir2/ snippyDir3/ ...

Options:

--help! This help.

—quiet! No output to stderr (default '0').

--verbose! Verbose output (default '0').

—inprefix=s Preferred input prefix of Snippy files (default 'snps').

--prefix=s

Output file prefix (default 'core').

—noref! Exclude reference (default '0').

--mincov=i

Minimum depth of coverage to consider core (default '10').

—aformat=s Output alignment format: nexus fasta phylip maf clustalw ... (default 'fasta').