Wenger, A.M. et al. Nat. Biotechnol. http://doi.org/dbgr (2019).
Long-read sequencing technologies have advantages in genome assembly, structural variant detection and haplotype phasing, but are less suited for single-nucleotide variant (SNV) and insertion/deletion (indel) calling due to the high error rate in comparison with short-read sequencing. Wenger et al., from Pacific Biosciences, optimized the circular consensus sequencing (CCS) protocol to achieve long, high-fidelity reads, in which they selected the SMRTbell library with fractions tightly distributed at 15 kb for high-coverage sequencing. The CCS library preparation was inspired and optimized based on their findings that polymerases have a better survival on damage-free DNA molecules. They employed the CCS protocol in sequencing the human genome (HG002) and achieved an average length of 13.5 kb, and an average accuracy of 99.8%. The CCS performance is comparable to, or better than, that of short-read sequencing in SNV and indel calling.
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Tang, L. Circular consensus sequencing with long reads. Nat Methods 16, 958 (2019). https://doi.org/10.1038/s41592-019-0605-6
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DOI: https://doi.org/10.1038/s41592-019-0605-6