DeepConsensus: Gap-Aware Sequence Transformers for Sequence Correction

Baid, G.; Cook, D. E.; Shafin, K.; Yun, T.; Llinares-Lopez, F.; Berthet, Q.; Wenger, A. M.; Rowell, W. J.; Nattestad, M.; Yang, H.; Kolesnikov, A.; Topfer, A.; Ammar, W.; Vert, J.-P.; Vaswani, A.; McLean, C. Y.; Chang, P.-C.; Carroll, A.

doi:10.1101/2021.08.31.458403

bioRxiv · 10.1101/2021.08.31.458403

DeepConsensus: Gap-Aware Sequence Transformers for Sequence Correction

Baid, G.·Cook, D. E.·Shafin, K.·Yun, T.·Llinares-Lopez, F.·Berthet, Q.·Wenger, A. M.·Rowell, W. J.·Nattestad, M.·Yang, H.·Kolesnikov, A.·Topfer, A.·Ammar, W.·Vert, J.-P.·Vaswani, A.·McLean, C. Y.·Chang, P.-C.·Carroll, A.

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Abstract

Pacific BioScience (PacBio) circular consensus sequencing (CCS) generates long (10-25 kb), accurate "HiFi" reads by combining serial observations of a DNA molecule into a consensus sequence. The standard approach to consensus generation uses a hidden Markov model (pbccs). Here, we introduce DeepConsensus, which uses a unique alignment-based loss to train a gap-aware transformer-encoder (GATE) for sequence correction. Compared to pbccs, DeepConsensus reduces read errors in the same dataset by 42%. This increases the yield of PacBio HiFi reads at Q20 by 9%, at Q30 by 27%, and at Q40 by 90%. With two SMRT Cells of HG003, reads from DeepConsensus improve hifiasm assembly contiguity (NG50 4.9Mb to 17.2Mb), increase gene completeness (94% to 97%), reduce false gene duplication rate (1.1% to 0.5%), improve assembly base accuracy (Q43 to Q45), and also reduce variant calling errors by 24%.

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Baid, G., Cook, D. E., Shafin, K., Yun, T., Llinares-Lopez, F., Berthet, Q., Wenger, A. M., Rowell, W. J., Nattestad, M., Yang, H., Kolesnikov, A., Topfer, A., Ammar, W., Vert, J.-P., Vaswani, A., McLean, C. Y., Chang, P.-C., Carroll, A.. 2021-08-31. DeepConsensus: Gap-Aware Sequence Transformers for Sequence Correction. https://doi.org/10.1101/2021.08.31.458403

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