Multi-pass sequencing

Abstract

Improved single molecule sequencing methods, compositions, and devices, are provided. In a first aspect, the present invention provides a multi-pass method of sequencing a target sequence using nanopore sequencing, the method comprising: i) providing a non-naturally occurring concatemer nucleic acid molecule comprising a plurality of copies of the target sequence; ii) nanopore sequencing at least three copies of the target sequence in the concatemer, thereby obtaining a multi-pass sequence dataset, wherein the multi-pass sequence dataset comprises target sequence datasets for the at least three copies of the target sequence; and iii) using the multi-pass sequence dataset to determine the target sequence.

Description

[0001] Cross References to Related Applications [0002] This application claims the benefit of and priority to US Provisional Application No. 62 / 078,306, filed November 11, 2014, the entire contents of which are incorporated herein by reference for all purposes. Background technique [0003] Single-molecule sequencing (SMS) methods, such as nanopore sequencing, have several advantages over other next-generation sequencing methods. In particular, SMS is fast and produces long read lengths. However, conventional SMS methods are characterized by high error rates in raw readings. The error rate can be expressed as % error, corresponding to the number of errors per 100 called bases. Alternatively, the error rate can be expressed as a "Q" value. "Q" can be calculated using the following formula: -10×log 10 (P), where P is the probability of a wrong base call. See Ewing & Green, 1998, Genome Res. 8: 186-194. For example, Q10 refers to a 1 / 10 probability of error, or 90% accura...

AI Technical Summary

Problems solved by technology

However, it is unclear whether this would lead to fewer errors, and there appear to be significant obstacles to actually implementing such a system