Quantify low complexity regions in DNA sequences I have fasta files with multiple sequences. They are reads that mapped to the genome outside of  probe-targeted regions.
From a quick perusal, they appear to be repetitive and have low complexity. Is there a way I can quantify their complexity and use that as an explanation as to why those regions were mapped to?
&quot;Complexity&quot; is also known as entropy. A quick and dirty way is to use a file compression utility - zip will get good compression for a repetitive sequence.
You can also look at the k-mer distribution for some suitable k: in a repetitive sequence it will be biased. Here is a tool that give a local plot: https://rdrr.io/github/vsbuffalo/qrqc/man/kmerEntropyPlot.html