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.