[tstactplsignore]

Fair points about both the memory requirement and Bowtie - also, 20 BP is really small, so while BLAT seems to find 20 BP hits correctly, it doesn't find 20 BP hits with mismatches. Why be so memory stringent? This is genomics, after all... If you're adverse to rolling your own, I'd look into BWA-MEM as a solution (which has more adjustable mismatch scoring than Bowtie), or figure out how Primer-BLAST seems to do specificity checks for small sequences so well.

[joshma]

We care about reducing memory usage because it gives us greater flexibility in our infrastructure. We're offering this to hundreds of scientists a day - not huge numbers in the grand scheme of things, but usage is bursty and by paying customers. This means we can mix in CRISPR work with our other processing infrastructure, and we can choose between many servers with low memory vs a few servers with high memory.

Maybe genomics doesn't have to be so memory hungry. 8)