Codes and instructions for comparing SubseqHash2 (SIMD version), minimizer, syncmer on mapping reads to reference genome.

• To generate random tables for SubseqHash2

  ../src/gentable_rc.out k d ./table_saving_path
  

  • ../src/gentable_rc.out k d ./table_saving_path generates random tables for SubseqHash2, where k is the length of subsequence, d is a parameter, and ./table_saving_path is the path of the file saving the tables. A sample file is at ./table_subseq2/25_11 with k=25 and d = 11. Slightly from the two previous expeirments, here we use the variant SubseqHash2r which requires to generate random tables that can produce the same seed for a string and its reverse complement.

• Data format: There are two data files. The first one is the reference genome of fasta format. It only has one sequence. There is an example at ./ref/sample. The second file is the read dataset with ground-truth. Each read takes two lines, the first line is the sequence. The second line is the ground-truth alignment, the i-th number $x_i$ in the second line means the i-th char of the read should be aligned to the position $x_i$. There is also an example ./reads/sample.

• Get results of SubseqHash2:

  • Seeding for reference genome ../src/refseeding_sub2.out n k d t table_file ref_file n, k, d are the parameter for SubseqHash2. ``tis the number of repeating times. The table file must be generated with the same parameters. ref_file` is the name of the reference genome. The output seeds are store at ./refseed/.

  • Seeding for reads ../src/readseeding_sub2.out n k d t table_file read_file. read_file is the name of the reference genome. The output seeds are store at ./readseed/.

  • Get seed matching results ../src/readmapping_sub2.out n k d t read_file. It will take the seeds from ./refseed and ./readseed. The output format is parameters, number of seed-matches, number of true seed-matches, ratio of true seed-matches, the average ratio of true seed-matches per read, number of 200bp segments, number of 200bp segments with true seed-matches, sensitivity of segments with true seed-matches.

  • An example on sample data:

    ../src/refseeding_sub2.out 30 25 11 2 ./table_subseq2/25_11 ./ref/sample
    ../src/readseeding_sub2.out 30 25 11 2 ./table_subseq2/25_11 ./reads/sample
    ../src/readmapping_sub2.out 30 25 11 2 ./reads/sample
    

• Get results of Other methods:

  • An example of minimizer on sample data. The arguments are k w ref_file read_file.

    ../src/readmapping_mini.out 25 5 ./ref/sample ./reads/sample
    

  • An example of syncmer on sample data. The arguments are k s ref_file read_file pos_1 pos_2 .. pos_s.

    ../src/readmapping_sync.out 20 10 ./ref/sample ./reads/sample 0 10
    

  • An example of CGK on sample data. The arguments are k t ref_file read_file where k is the length of k-mer, t is the number of repeats.

    ../src/readmapping_cgk.out 20 5 ./ref/sample ./reads/sample
    

  • An example of syncmer on sample data. The arguments are k n w_min w_max t ref_file read_file. k is the length of substring, n is the number of substrsings to be concatenated, w_min and w_max are the positions for the window, t is the number of repeating times

    ../src/readmapping_stro.out 10 2 10 20 2 ./ref/sample ./reads/sample