IDentity with Locality: An ideal hash for efficient gene sequence search --- the official code repository

Please follow the instructions below for reproducing the experiments. The code is tested on a machine running Ubuntu 20.04 with CMake 3.16.3 and GNU Make 4.2.1.

1. Download the data files using SRA toolkit. For installing SRA toolkit use this guide https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
2. Download the sequence files to data/ folder:

cd data
fastq-dump ERR337856 -O .
cd ..

3. Build the program:

mkdir build && cd build
cmake .. && make -j
cd ..

4. Run all experiments for vanilla Bloom filters vs IDL-Bloom filters, with the results written into results folder

mkdir results
bash run.sh

5. To run all experiments for vanilla COBS vs IDL-COBS, switch to the abf branch by using git checkout abf and follow the instructions in README.md to run the experiments.