a long read repeat coverage calculator,given an long read file before assembly either direct from the sequencing runs or after the cleaning, it calculates the total amount of the repeat stretches present in the sequencing reads and you can plot them before assembly to see how much repetitive your sequencing is and how to set the long read assembly parameters.
I implemented a totally different approach and it parses millions of long reads in few minutes for the estimation of the coverage. It reports where the stretch is located and what is the position and how much is the total coverage of that type in your each sequencing read.
repeatlocatorLongRead("/Users/gauravsablok/Desktop/CodeCheck/test_sample_sample1.fasta",
polyATGCstretch_type="A")
ids sequences repeat_locator fraction_length fraction_length_coverage
0 >seq1 ATATATATATAAGACGAGATAATAAAATTTTATATATATATAAAAA... [AAAA, AAAAA] [(41, 46), (23, 27)] 5.777778
1 >seq2 ATATATATATAAGACGAGATAATAAAATTTTATATATATATAAAAA... [AAAA, AAAAA] [(41, 46), (23, 27)] 5.777778
Gaurav
Academic Staff Member
Bioinformatics
Institute for Biochemistry and Biology
University of Potsdam
Potsdam,Germany