To run the code for datasets without errors:

python assembler.py input_file kmer_size

kmer_size is a range of values, so it can run multiple kmer size at once. It should be formatted like start-end.

To run the code for datasets with errors:

python assembler.py input_file kmer_size error_threshold

error_threshold is basically the number of time a kmer appears. When generating kmers from reads, an error in a read will result in a kmer that does not appear as often as other kmers. Try different error_threshold values to see if longest contig length changes.

To output to a file for easier reading, pipe stdout to file:

python assembler.py input_file kmer_size [error_threshold] > output_file

To run the mapping project:

python mapper.py genome_file reads_file thread_count

thread_count is the number of cores you'd like to run this program on (for speed-up purposes). Note: if any of the arguments are missing the program will fail. To output to a SAM file to use with samtools:

python mapper.py genome_file reads_file thread_count > file_name.sam

To run the mapping project with errors:

python mapper.py genome_file reads_file thread_count kmer_size

kmer_size is the size of the kmer a read will be broken down into for error handling.