sparc

The algorithm developed for Bioinformatics class based on: Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads

Running

1. Get the code

Clone this repository
cd sparc

2. Download the data and install graphmap

chmod +x ./prepare_data.sh
./prepare_data.sh

3. Run the algorithm

3.a lambda

chmod +x ./run.sh
./run.sh lambda 1

3.b ecoli

chmod +x ./run.sh
./run.sh ecoli 1

The second argument for run.sh script is number of iterations.