| Meno: | Matej
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| Priezvisko: | Fedor
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| Názov: | Monitoring and Controlling Nanopore Sequencing Runs
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| Vedúci: | doc. Mgr. Tomáą Vinař, PhD.
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| Rok: | 2023
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| Kµúčové slová: | sequencing, adaptive, emulator, sampling
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| Abstrakt: | Modern nanopore sequencers provide users with the option to decide if a DNA sequence is rejected or sequenced. Decisions are made based on the
raw nanopore signal in real time. This feature of nanopore sequencers is called selective sequencing.
One can increase the sequencing coverage by adaptively sampling the desired DNA sequences and rejecting the undesired ones.
The potential coverage gain achieved by adaptive sampling increases with the decision speed. Various methods to perform adaptive
sampling are currently being researched.
We facilitate the development and testing of adaptive sampling tools by introducing a sequencing emulator capable of emulating
the selective sequencing. We describe in detail the development of the emulator and demonstrate its use in combination with a
well-known adaptive sampling tool. We also study the potential use of machine learning for adaptive sampling.
We propose a convolutional neural network classifier that makes fast decisions about sequenced DNA. We compare the classifier
with another adaptive sampling tool and present our findings.
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