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bioRxiv · 10.1101/2021.11.19.469328

Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim

Yang, C.·Lo, T.·Nip, K. M.·Hafezqorani, S.·Warren, R. L.·Birol, I.
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Abstract

Nanopore sequencing is crucial to metagenomic studies as its kilobase-long reads can contribute to resolving genomic structural differences among microbes. However, platform-specific challenges, including high base-call error rate, non-uniform read lengths, and the presence of chimeric artifacts, necessitate specifically designed analytical tools. Here, we present Meta-NanoSim, a fast and versatile utility that characterizes and simulates the unique properties of nanopore metagenomic reads. Further, Meta-NanoSim improves upon state-of-the-art methods on microbial abundance estimation through a base-level quantification algorithm. We demonstrate that Meta-NanoSim simulated data can facilitate the development of metagenomic algorithms and guide experimental design through a metagenomic assembly benchmarking task.

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Yang, C., Lo, T., Nip, K. M., Hafezqorani, S., Warren, R. L., Birol, I.. 2021-11-20. Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim. https://doi.org/10.1101/2021.11.19.469328

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