Validation of sycnmers compared to minimizers
There is a Makefile. It will build the binary, but it does not have header file dependencies so be careful if you edit headers. You need the gcc compiler. There are no dependencies on third-party libraries. The Makefile uses ccache, if you don't have ccache installed then edit the Makefile to delete it.
There is a Microsoft Visual Studio project file for VS 2017 (v15.4). This will probably work if imported into newer VS versions, I didn't test this.
syncmer -newbench output.tsv [options]
Metrics are written to output.tsv in tab-separarated text format. Options:
-k nn or -klo nn -khi nn Value(s) of k to test (k-mer length).
-s nn or -slo nn -klo nn Value(s) of s (syncmer substring length).
-w nn or -wlo nn -whi nn Values(s) of w (minimizer window length).
-d nn Integer down-sampling parameter.
-pctid nn or -pctidlo nn -pctidhi nn -pctidinc nn Mutation rate(s).
-seqlength nn Random sequence length. Default 1000000.
-pcitidout pctid.tsv Writes pctid metrics to tabbed file.
spacingout spacing.tsv Writes spacing frequencies to tabbed file.
If the lo & hi variants of an option are specified, then all values from lo to hi are tested.
syncmer -newbench results.tsv -k 15 -m 10 -pctidlo 75 -pctidhi 95 -pcitidinc 5
syncmer -newbench results.tsv -k 15 -slo 2 -shi 13 -pctidlo 80 -pctidhi 90 -pcitidinc 10
sycnmer -searchsix genome1.fasta -db genome2.fasta -sts ST -k K -w W -t T -log results.txt
ST is the submer type: Minimizer1 for minimizers or Syncmer5 for syncmers. K is the kmer length, W is the minimizer window length, T is the syncmer substring length (same as -s parameter for -newbench command).