An error-correction code (ECC) sequencing approach has recently been reported to effectively reduce sequencing errors by interrogating a DNA fragment with three orthogonal degenerate sequencing-by-synthesis (SBS) reactions. However, similar to other non-single-molecule SBS methods, the reaction will gradually lose its synchronization within a molecular colony in ECC sequencing. This phenomenon, called dephasing, causes sequencing error, and in ECC sequencing, induces distinctive dephasing patterns. To understand the characteristic dephasing patterns of the dual-base flowgram in ECC sequencing and to generate a correction algorithm, we built a virtual sequencer in silico. Starting from first principles and based on sequencing chemical reactions, we simulated ECC sequencing results, identified the key factors of dephasing in ECC sequencing chemistry and designed an effective dephasing algorithm. The results show that our dephasing algorithm is applicable to sequencing signals with at least 500 cycles, or 1000-bp average read length, with acceptably low error rate for further parity checks and ECC deduction. Our virtual sequencer with our dephasing algorithm can further be extended to a dichromatic form of ECC sequencing, allowing for a potentially much more accurate sequencing approach.

中文翻译：

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虚拟测序仪揭示了纠错码 DNA 测序中的移相模式

最近有报道称，一种纠错码 (ECC) 测序方法可通过三个正交简并合成测序 (SBS) 反应来查询 DNA 片段，从而有效减少测序错误。然而，与其他非单分子 SBS 方法类似，在 ECC 测序中，该反应将逐渐失去其分子集落内的同步。这种称为去相位的现象会导致测序错误，并且在 ECC 测序中，会导致独特的去相位模式。为了了解 ECC 测序中双碱基流程图的特征移相模式并生成校正算法，我们在计算机上构建了一个虚拟测序仪. 我们从第一性原理出发，基于测序化学反应，模拟ECC测序结果，确定ECC测序化学中去相的关键因素，设计了有效的去相算法。结果表明，我们的去相算法适用于至少 500 个循环或 1000 bp 平均读取长度的测序信号，具有可接受的低错误率，用于进一步的奇偶校验和 ECC 推导。我们的带有去相算法的虚拟测序仪可以进一步扩展到 ECC 测序的二色形式，从而实现潜在更准确的测序方法。