I have a list of kmers, between 8-12 nt in length, and I would like to align these to a larger sequence returning all ungapped matches with at most 2 mismatches. I would like search to be exhaustive i.e. I do not want to miss anything. I wrote a python script to compute hamming distance for all substrings of my reference to the query, but it is too slow for many (1000s) queries on a reference of ~100,000nt.
What program would you recommend that does this and runs rather quickly. I have looked into Bowtie2, but I am unsure if it was designed to work with such short query sequences.
Thanks for the feedback.