https://github.com/edawson/mkmh

Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.
https://github.com/edawson/mkmh

kmer locality-sensitive-hashing minhash

Last synced: about 2 months ago
JSON representation

Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.

• Host: GitHub
• URL: https://github.com/edawson/mkmh
• Owner: edawson
• License: mit
• Created: 2016-06-16T14:32:52.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2021-01-09T01:42:34.000Z (almost 4 years ago)
• Last Synced: 2023-04-04T14:14:19.668Z (almost 2 years ago)
• Topics: kmer, locality-sensitive-hashing, minhash
• Language: C++
• Homepage:
• Size: 204 KB
• Stars: 23
• Watchers: 2
• Forks: 2
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# mkmh

Make kmers, minimizers, hashes, and MinHash sketches (with multiple k), and compare them. 

![C/C++ CI for mkmh](https://github.com/edawson/mkmh/workflows/C/C++%20CI/badge.svg)

## Usage

To use mkmh functions in your code:  

1. Include the header file in your code  

    ```#include "mkmh.hpp"```      

2. Compile the library:  

    `` cd mkmh && make lib``  

3. 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  

4. That's it!

## Available functionality

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.

## Getting help

Please reach out through [github](https://github.com/edawson/mkmh) by posting an issue (even if it's just feedback). Email is acceptable as a secondary medium.