Error Correction Algorithm for Biological Sequences
Please, compile the source code revised_ec.cpp with the following command using g++ compiler (gcc version 4.6.1 or above): g++ -O3 revised_ec.cpp -o ec
The command will produce an executable file named ec. Please, run the following command to correct the reads:
./ec <input_file_name> <output_file_name>
Please, note that input file will be FASTA file where the format of the file should be:
read_id read_string read_id read_string . . .
The corrected reads will be placed in output_file as FASTA format. If you want to tune the parameters, please, find initialize_parameters() function block at the beginning of the source code and change the parameters accordingly.