Could you help me bioinformatics SE people.
So I have been duckduckgo-ing up a storm and even consulted the AI overlords and haven't come up with a solid way to do this, but it is so fundamental to bioinformatics that it has to already exists and I don't need to be re-inventing the wheel...
So imagine you have a fasta/q file with a "reference" sequence:
And a list of short oligo sequences:
TTTT, CCCC, GGGG
How would be the best way to map (if that is the right terminology) the short oligos to the reference seq so that a configurable mismatch amount is allowed:
TTTT CCCC GGGG CCCC
Blast, BWA and Bowtie2 from my understanding aren't ideal for this because they aren't built for really short sequences, something about them using seeded reference lookup? Using Smith-Watterman or Needleman-Wunsch technically gets the local aligning right but the mismach allowance is based on score not X total allowed. Plus, iterating over hundreds of oligos and aligning against dozens of large references seems inefficient. The closest thing I have found to what I'm trying to do is Sequence Manipulation Suites' Primer Map. This tool is almost perfect except a) it is a web tool, not a module I could import into python or incorporate into a CLI and b) does not appear to offer any tolerance for mismatches.
Am I just searching with the wrong vocabulary? This has to be an already solved bioinformatics process right?