DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer
Circular consensus sequencing with Pacific Biosciences technology generates long , accurate ‘HiFi’ reads by combining serial observations of a DNA molecule into a consensus sequence. The standard approach to consensus generation, pbccs, uses a hidden Markov model. We introduce DeepConsensus, which uses an alignment-based loss to train a gap-aware transformer–encoder for sequence correction. Compared to pbccs, DeepConsensus reduces read errors 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 to 17.2 Mb), increase gene completeness , reduce the false gene duplication rate , improve assembly base accuracy and reduce variant-calling errors by 24%.
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