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CMU-SAFARI / RawAlign

RawAlign is a real-time raw nanopore read mapper based on the Seed-Filter-Align paradigm as described by Lindegger et al. (https://arxiv.org/abs/2310.05037)
https://arxiv.org/abs/2310.05037
GNU General Public License v3.0
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Difference between Rawhash and Rawalign #2

Open xianyu0623 opened 3 months ago

xianyu0623 commented 3 months ago

Hello!

I am currently exploring the fantastic algorithms developed by your team. However, I have a question regarding the difference between Rawhash and Rawalign. From my understanding, both Rawhash and Rawhash 2 are focused on read-wise alignment by using hash-based method, whereas Rawalign is capable of achieving base-wise alignment by additional DTW. Is my understanding correct?

joellindegger commented 2 months ago

Hi

RawHash proposed the hash-based seeding method that was reused in RawAlign, and RawAlign indeed adds base-wise (or event-wise) alignment using DTW. RawAlign can use DTW to improve mapping accuracy and/or put this event-wise alignment in the resulting .paf file.

The latest version of RawHash (RawHash2) includes RawAlign's DTW implementation. Due to changes in the seeding and chaining algorithms in RawHash2 compared to RawHash, currently RawAlign is slightly more accurate than the overall combination of RawHash2 with DTW. However, we expect to soon achieve the same or higher accuracy with RawHash2 and DTW by optimizing the DTW implementation and parameters.