shao-group / subseqhash

Introduction

SubseqHash is a seeding method that uses minimized subsequence as seeds. This repository provides source code for 5 different experiments in different folders. The folder ordering contains code for generating an A/B/C order and computing the similarity of neighboring strings in an order. hashcollision contains code for computing the probability of hash collision of different methods. pariwisealignment has code for using SubseqHash in pairwise sequence alignment. readmaping has code for mapping reads to reference genome with SubseqHash. overlap-detection provides code for comparing SubseqHash with minimizer on the seeding step of overlap detection.

Usage

The repository can be installed with following command. The detailed instruction of each experiment can be found in the corresponding folder.

git clone https://github.com/Shao-Group/subseqhash.git