AI Article Synopsis
- Scientists developed a new way called DeepConsensus to help correct DNA sequences more accurately than an older method called pbccs.
- DeepConsensus uses advanced technology to lower errors in the DNA reads by 42%, which means it helps make the sequencing more reliable.
- This new approach not only improves the quality of the DNA readings but also enhances how genes are understood and reduces mistakes in identifying genetic variations.
Article Abstract
Circular consensus sequencing with Pacific Biosciences (PacBio) technology generates long (10-25 kilobases), 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 (NG50 4.9 megabases (Mb) to 17.2 Mb), increase gene completeness (94% to 97%), reduce the false gene duplication rate (1.1% to 0.5%), improve assembly base accuracy (Q43 to Q45) and reduce variant-calling errors by 24%. DeepConsensus models could be trained to the general problem of analyzing the alignment of other types of sequences, such as unique molecular identifiers or genome assemblies.
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| http://dx.doi.org/10.1038/s41587-022-01435-7 | DOI Listing |
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