ska compare

SKA compare

The compare subcommand prints some comparison statistics of a query split kmer file against a set of subject split kmer files.

Output columns

Column	Description
Subject	The name of the split kmer subject file being compared to the query file
Kmers unique to Query	Number of kmers found only in the query split kmer file
Kmers unique to Subject	Number of kmers found only in the subject split kmer file
Matches	Number of kmers matching between the files
% kmers in Query matching	Percentage of query kmers that match a subject kmer
% kmers in Subject matching	Percentage of subject kmers that match a query kmer
SNPs	Number of SNPs between the middle bases of the matching split kmers
%ID of matching kmers	Percentage of matching split kmers with a SNP
%ID of query kmers	Percentage of query kmers that match a subject kmer with a SNP
%ID of subject kmers	Percentage of subject kmers that match a query kmer with a SNP
Ns in Query	Number of split kmers with an N as the middle base in the query only
Ns in Subject	Number of split kmers with an N as the middle base in the subject only
Ns in both	Number of split kmers with an N as the middle base in both

Usage

ska compare [options] <subject split kmer files>

Options:
-h		Print this help
-f <file>	File of split kmer file names. These will be added to or 
		used as an alternative input to the list provided on the 
		command line.
-q <file>	Query split kmer file