I am in need of using Bowtie2 to find all possible alignments for a set of reads (each 23bp long) to the human genome. The maximum number of mismatches that can be tolerated is 6. But since Bowtie2 allows mismatches only upto 1, I had to set the mismatch penalty for alignment score accordingly to get the result. Since my laptop does not have the capacity to perform this operation, I am searching for interfaces that provide access to Bowtie2. I found Galaxy to be useful but unfortunately, I cannot see an option to set the alignment score in it. Does anyone know of any other tool that provides an option for Bowtie2 with alignment score?