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This is patronizing to say a programmer could write algorithms that are complex enough there is a major dedicated to it at most universities. You have to realiz
by alacritas0 4y ago
This is patronizing to say a programmer could write algorithms that are complex enough there is a major dedicated to it at most universities. You have to realize that you're probably thinking of using a naive solution that produces an extra another order of runtime complexity for datasets that reach 100GB easily.
- jefftk 4y agoThe complexity comes from trying to do it efficiently, both in using the hardware well and in squeezing as much data as possible out of the sequencing reads you have. But if you relax both of those it's a manageable problem for an amateur.
- alacritas0 4y agoEfficiency is crucial though. Running cutting edge published alignment tools running on the best AWS server will take hours to process a 30x human genome. An amateur approach for NGS on anything but a model organism would take years or decades to finish alignment on current hardware.
- jefftk 4y agoPart of why the best tools take so long is that they are trying really hard, but an amateur approach can do a decent job in far less time by trying less hard. (No fuzzy matching, only exact matching on shortish chunks) Additionally, we're talking about nanopore data, which is much longer reads, and so is going to be computationally a bit easier.