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ZENODO
Dataset . 2021
License: CC BY
Data sources: Datacite
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ZENODO
Dataset . 2021
License: CC BY
Data sources: ZENODO
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ZENODO
Dataset . 2021
License: CC BY
Data sources: Datacite
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Simulated wastewater sequencing data for benchmarking SARS-CoV-2 variant abundance estimation

Authors: Baaijens, Jasmijn A.; Zulli, Alessandro; Ott, Isabel M.; Petrone, Mary E.; Alpert, Tara; Fauver, Joseph R.; Kalinich, Chaney C.; +19 Authors

Simulated wastewater sequencing data for benchmarking SARS-CoV-2 variant abundance estimation

Abstract

To evaluate the accuracy of variant abundance predictions from wastewater sequencing, we built a collection of benchmarking datasets that resemble real wastewater samples. For each variant (B.1.1.7, B.1.351, B.1.427, B.1.429, P.1) we created a series of 33 benchmarks by simulating sequencing reads from a variant genome, as well as a collection of background (non-variant of concern/interest) sequences, such that the variant abundance ranges from 0.05% to 100%. Analogously, we created a second series of benchmarks, simulating reads only from the Spike gene of each SARS-CoV-2 genome. We refer to the first set of benchmarks as "whole genome" (WG) and to the second set of benchmarks as "S-only". We repeated these simulations at different sequencing depths: 100x and 1000x coverage for the whole genome benchmarks, and 100x, 1000x, and 10,000x coverage for the S-only benchmarks.

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Keywords

SARS-CoV-2 variants, computational biology, wastewater sequencing

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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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