ska compare - simonrharris/SKA GitHub Wiki
The compare subcommand prints some comparison statistics of a query split kmer file against a set of subject split kmer files.
| 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 |
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