Implementation of implicit compressed de Bruijn graph.
Project for bioinformatics course on Faculty of Electrical Engineering and Computing, Zagreb.
[Tena Perak] (https://github.com/tenap)
[Katarina Matić] (https://github.com/qwertzuio40)
[Dino Rakipović] (https://github.com/drakipovic)
git clone [email protected]:simongog/sdsl-lite.git sdsl-lite
cd sdsl-lite
./install.sh [PATH]
export SDSLLITE=[PATH]
git clone https://github.com/drakipovic/de-brujin-graph
cd de-brujin-graph
make
This compiles the code and creates bin/main executable.
bin/main input_file output_file --option -k={int}
input_file is absoulte path to input file in fasta format
output_file is absolute path to output file.
options are
--implicit
--explicit
--bitvector
implicit prints only implicit graph
explicit prints only explicit graph
bitvector prints only bit vectors
{int} is size of k-mer.
chmod +x run_tests.py
./run_tests.py
MIT License
Copyright (c) Katarina Matic, Tena Perak, Dino Rakipovic