US 11,851,704 B2
Deepsimulator method and system for mimicking nanopore sequencing
Xin Gao, Thuwal (SA); Yu Li, Thuwal (SA); Sheng Wang, Thuwal (SA); and Renmin Han, Thuwal (SA)
Assigned to KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY, Thuwal (SA)
Filed by KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY, Thuwal (SA)
Filed on Jun. 23, 2021, as Appl. No. 17/355,823.
Application 17/355,823 is a continuation of application No. 16/769,127, granted, now 11,078,531, previously published as PCT/IB2018/058502, filed on Oct. 30, 2018.
Claims priority of provisional application 62/702,161, filed on Jul. 23, 2018.
Claims priority of provisional application 62/599,908, filed on Dec. 18, 2017.
Claims priority of provisional application 62/598,086, filed on Dec. 13, 2017.
Prior Publication US 2021/0317523 A1, Oct. 14, 2021
This patent is subject to a terminal disclaimer.
Int. Cl. G01N 33/48 (2006.01); G01N 33/50 (2006.01); C12Q 1/6869 (2018.01); G16B 40/30 (2019.01); G16B 40/10 (2019.01); G16B 30/20 (2019.01); G06N 3/088 (2023.01)
CPC C12Q 1/6869 (2013.01) [G06N 3/088 (2013.01); G16B 30/20 (2019.02); G16B 40/10 (2019.02); G16B 40/30 (2019.02)] 20 Claims
OG exemplary drawing
 
1. A method for simulating reads for a sequencing technology of biopolymers that uses nanopores, the method comprising:
generating, with a sequence generator module, an input nucleotide sequence having plural k-mers, wherein the input nucleotide sequence satisfies coverage and length distribution associated with the sequencing technology that uses the nanopores;
simulating with a deep learning simulator, actual electrical current signals corresponding to the input nucleotide sequence;
identifying reads that correspond to the actual electrical current signals; and
displaying the reads,
wherein the deep learning simulator includes a context-dependent deep learning model that takes into consideration a position of a k-mer of the plural k-mers on the input nucleotide sequence when calculating a corresponding actual electrical current.