I would like to be able to align around 500 short sequences (~20 nucleotides) to the human genome in a super quick way.
I would like to authorize up to 5 mismatches but no gaps. I also would like to retrieve all possible hits for one sequence... not just the best ones. Then, I would like to be able to annotate the hits.
I will need to repeat this work very often.
I investigated the NGS tools like bowtie or BWA to see if I could tweak them but it seems that the number of mismatches are limited to 3 and 1 respectively...this is a pity because it would have been great to have the results in a SAM format to do the follow up annotation step!
Could anyone advise me one a very fast aligner to do what I would like please?