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GeorgetteTanner / w-Wessim2

A tool for in silico whole-exome sequencing.
GNU General Public License v3.0
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Question: thoughts on replacing BLAT with minimap2? #5

Open ajw2329 opened 2 months ago

ajw2329 commented 2 months ago

Hello!

Thanks again for your great tool. I wondering what your thoughts were on the idea of replacing BLAT/pblat with a tool like minimap2 for probe alignment.

I've been experimenting with it, and on the one hand it is radically faster than blat/pblat, but the alignments, while reasonable so far on random inspection, are not the same. I expect it might be tricky to get the exact right settings. Any thoughts would be much appreciated!

GeorgetteTanner commented 2 months ago

Hello Thanks for the interesting question! I haven't experimented with other aligners myself. Blat was initially used in the original w-Wessim method when hybridisation probe sequences were used, and in that scenario you would ideally want to perform the alignment in a way that allows for off-target alignments in order to capture "leaky" exon enrichment. I found that wasn't feasible with BLAT and so went down the route of using real WES read sequences as the probes to force the same pattern of reads. In this case you probably just want accurate alignments of the "probes" (as the off-target effect has already been captured in the real reads), and I would expect that using the same aligner as you would downstream when aligning the simulated reads would be optimum. With any other aligner you potentially just increase the overall error. So yes minimap2 may be a more suitable choice, particularly given its speed. I'd be interested to hear how you get on with it!