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

Autor: Yang C; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada.; Bioinformatics Graduate Program, University of British Columbia, Genome Sciences Centre, BCCA 100-570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada., Lo T; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada.; Bioinformatics Graduate Program, University of British Columbia, Genome Sciences Centre, BCCA 100-570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada., Nip KM; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada.; Bioinformatics Graduate Program, University of British Columbia, Genome Sciences Centre, BCCA 100-570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada., Hafezqorani S; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada.; Bioinformatics Graduate Program, University of British Columbia, Genome Sciences Centre, BCCA 100-570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada., Warren RL; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada., Birol I; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada.; Department of Medical Genetics, University of British Columbia, Life Sciences Centre Room 1364 - 2350 Health Science Mall Vancouver, BC V6T 1Z3, Canada.
Jazyk: angličtina
Zdroj: GigaScience [Gigascience] 2023 Mar 20; Vol. 12. Date of Electronic Publication: 2023 Mar 20.
DOI: 10.1093/gigascience/giad013
Abstrakt: Background: Nanopore sequencing is crucial to metagenomic studies as its kilobase-long reads can contribute to resolving genomic structural differences among microbes. However, sequencing platform-specific challenges, including high base-call error rate, nonuniform read lengths, and the presence of chimeric artifacts, necessitate specifically designed analytical algorithms. The use of simulated datasets with characteristics that are true to the sequencing platform under evaluation is a cost-effective way to assess the performance of bioinformatics tools with the ground truth in a controlled environment.
Results: Here, we present Meta-NanoSim, a fast and versatile utility that characterizes and simulates the unique properties of nanopore metagenomic reads. It improves upon state-of-the-art methods on microbial abundance estimation through a base-level quantification algorithm. Meta-NanoSim can simulate complex microbial communities composed of both linear and circular genomes and can stream reference genomes from online servers directly. Simulated datasets showed high congruence with experimental data in terms of read length, error profiles, and abundance levels. We demonstrate that Meta-NanoSim simulated data can facilitate the development of metagenomic algorithms and guide experimental design through a metagenome assembly benchmarking task.
Conclusions: The Meta-NanoSim characterization module investigates read features, including chimeric information and abundance levels, while the simulation module simulates large and complex multisample microbial communities with different abundance profiles. All trained models and the software are freely accessible at GitHub: https://github.com/bcgsc/NanoSim.
(© The Author(s) 2023. Published by Oxford University Press GigaScience.)
Databáze: MEDLINE
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