For generating simulated data:

• generate_random_fasta.py: generates num_sequences random sequence over the ACGT alphabet, fasta format. The user defines the average and minimal size of sequences generate_random_fasta.py num_sequences average_size min_size output_file

• extract_random_sequences.py Extracts sequences from a fasta of fastq file. extract_random_sequences.py [-h] --input INPUT_FILE --min_size MIN_SIZE --max_size MAX_SIZE --num NUM_SEQUENCES --output OUTPUT_FILE

• yield_reads.py and revcomp.py are for internal use.

For parsing back_to_sequences results:

• filter_reads.pyon back_to_sequences results: conserve only reads whose percent of conserved kmers is at least equals to threshold filter_reads.py file threshold