Dataset Information

Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing.

ABSTRACT: We develop a general computational approach for improving the accuracy of basecalling with Oxford Nanopore's 1D² and related sequencing protocols. Our software PoreOver ( https://github.com/jordisr/poreover ) finds the consensus of two neural networks by aligning their probability profiles, and is compatible with multiple nanopore basecallers. When applied to the recently-released Bonito basecaller, our method reduces the median sequencing error by more than half.

SUBMITTER: Silvestre-Ryan J

PROVIDER: S-EPMC7814537 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing.

Silvestre-Ryan Jordi J Holmes Ian I

Genome biology 20210119 1

We develop a general computational approach for improving the accuracy of basecalling with Oxford Nanopore's 1D<sup>2</sup> and related sequencing protocols. Our software PoreOver ( https://github.com/jordisr/poreover ) finds the consensus of two neural networks by aligning their probability profiles, and is compatible with multiple nanopore basecallers. When applied to the recently-released Bonito basecaller, our method reduces the median sequencing error by more than half. ...[more]

PMID: 33468205

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Project description:Insects and vertebrates harbor specific neurons that encode the animal's head direction (HD) and provide an internal compass for spatial navigation. Each HD cell fires most strongly in one preferred direction. As the animal turns its head, however, HD cells in rat anterodorsal thalamic nucleus (ADN) and other brain areas fire already before their preferred direction is reached, as if the neurons anticipated the future HD. This phenomenon has been explained at a mechanistic level, but a functional interpretation is still missing. To close this gap, we use a computational approach based on the movement statistics of male rats and a simple model for the neural responses within the ADN HD network. Network activity is read out using population vectors in a biologically plausible manner, so that only past spikes are taken into account. We find that anticipatory firing improves the representation of the present HD by reducing the motion-induced temporal bias inherent in causal decoding. The amount of anticipation observed in ADN enhances the precision of the HD compass read-out by up to 40%. More generally, our theoretical framework predicts that neural integration times not only reflect biophysical constraints, but also the statistics of behaviorally relevant stimuli; in particular, anticipatory tuning should be found wherever neurons encode sensory signals that change gradually in time.SIGNIFICANCE STATEMENT Across different brain regions, populations of noisy neurons encode dynamically changing stimuli. Decoding a time-varying stimulus from the population response involves a trade-off: For short read-out times, stimulus estimates are unreliable as the number of stochastic spikes is small; for long read-outs, estimates are biased because they lag behind the true stimulus. We show that optimal decoding of temporally correlated stimuli not only relies on finding the right read-out time window but requires neurons to anticipate future stimulus values. We apply this general framework to the rodent head-direction system and show that the experimentally observed anticipation of future head directions can be explained at a quantitative level from the neuronal tuning properties, network size, and the animal's head-movement statistics.

Dataset Information

Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing.

Publications

Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing.

Similar Datasets

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