Make kmers, minimizers, hashes, and MinHash sketches (with multiple k), and compare them.
To use mkmh functions in your code:
- Include the header file in your code
#include "mkmh.hpp" - Compile the library:
cd mkmh && make lib - Make sure the lib and header are on the LD include/lib paths (e.g. in your makefile):
`` gcc -o my_code my_code.cpp -L/path/to/mkmh -I/path/to/mkmh -lmkmh - That's it!
Convenience functions:
- Reverse complement a string
- Reverse a string
- Capitalize the characters of a string
- Check if a string contains only canonical DNA letters ("A", "a", "C", "c", "T", "t", "G", "g")
Substrings and transforms:
- Get the forward shingles of a string
- Get the kmers size k of a string
- For multiple k, Get the kmers of a string for all k
- Get the (w, k) minimizers of a string
- Calculate the 64-bit hashes of the kmers of a string (with either single or multiple k values)
- Get the MinHash sketch of a string (from either single or multiple k values), using either the top s hashes or the bottom s hashes.
Compare sets of shingles / kmers / minimizers / hashes:
- Take the union of two sets of kmers or hashes.
- Take the intersection of two sets of kmers or hashes.
Fun extras:
- Given a string and a set of query strings, sort the queries in order
of percent similarity.
Please reach out through github by posting an issue (even if it's just feedback). Email is acceptable as a secondary medium.