Working on a fastQ file, I would like to get the occurrences of repeated sequences for all possible kmers of a given length that cover at least 90% of the read's length for the whole data set.
for a length 6 with the kmer "ATTGGG" and a data set containing reads of 300 bases each
I want to obtain the occurrences of the following kmers :
ATTGGGATTGGGATTGGGATTGGGATTGGGATTGGG...... (90 % of the read's length without gaps) ATTGGGATTGGGATTGGGATTGGGATTGGGATTGGGA..... (91%) ATTGGGATTGGGATTGGGATTGGGATTGGGATTGGGAT.... (92%)
this for all possible combinations of kmers of length = 6.
I have done some research and tested many softwares such as (KMC2,Jellyfish,Khmer,Dsk,Scturtle) but none matched what I would like to do, because I want to obtain the occurrences of the repeated kmer without any possible gaps in-between with a certain % of read coverage.
I've done a naive algorithm that works but the optimization isn't the best obviously. Is there a tool that does the trick ?