I have paired-end whole genome sequencing data, and I would like to try finding STRs (Short Tandem Repeats) in this data. What tools should I use? There is no assembled reference genome available for my species.
That will mask (to lowercase) sequences with STRs with repeating subunits of length between 1 and 15. Then you can filter the reads with lowercase letters in them... I don't have a program for that though.