Enhancing Long-Read-Based Strain-Aware Metagenome Assembly

Luo X, Kang X, Schönhuth A (2022)
Frontiers in Genetics 13: 868280.

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Abstract / Bemerkung
Microbial communities are usually highly diverse and often involve multiple strains from the participating species due to the rapid evolution of microorganisms. In such a complex microecosystem, different strains may show different biological functions. While reconstruction of individual genomes at the strain level is vital for accurately deciphering the composition of microbial communities, the problem has largely remained unresolved so far. Next-generation sequencing has been routinely used in metagenome assembly but there have been struggles to generate strain-specific genome sequences due to the short-read length. This explains why long-read sequencing technologies have recently provided unprecedented opportunities to carry out haplotype- or strain-resolved genome assembly. Here, we propose MetaBooster and MetaBooster-HiFi, as two pipelines for strain-aware metagenome assembly from PacBio CLR and Oxford Nanopore long-read sequencing data. Benchmarking experiments on both simulated and real sequencing data demonstrate that either the MetaBooster or the MetaBooster-HiFi pipeline drastically outperforms the state-of-the-art de novo metagenome assemblers, in terms of all relevant metagenome assembly criteria, involving genome fraction, contig length, and error rates. Copyright © 2022 Luo, Kang and Schonhuth.
Erscheinungsjahr
2022
Zeitschriftentitel
Frontiers in Genetics
Band
13
Art.-Nr.
868280
eISSN
1664-8021
Page URI
https://pub.uni-bielefeld.de/record/2963686

Zitieren

Luo X, Kang X, Schönhuth A. Enhancing Long-Read-Based Strain-Aware Metagenome Assembly. Frontiers in Genetics. 2022;13: 868280.
Luo, X., Kang, X., & Schönhuth, A. (2022). Enhancing Long-Read-Based Strain-Aware Metagenome Assembly. Frontiers in Genetics, 13, 868280. https://doi.org/10.3389/fgene.2022.868280
Luo, Xiao, Kang, Xiangbin, and Schönhuth, Alexander. 2022. “Enhancing Long-Read-Based Strain-Aware Metagenome Assembly”. Frontiers in Genetics 13: 868280.
Luo, X., Kang, X., and Schönhuth, A. (2022). Enhancing Long-Read-Based Strain-Aware Metagenome Assembly. Frontiers in Genetics 13:868280.
Luo, X., Kang, X., & Schönhuth, A., 2022. Enhancing Long-Read-Based Strain-Aware Metagenome Assembly. Frontiers in Genetics, 13: 868280.
X. Luo, X. Kang, and A. Schönhuth, “Enhancing Long-Read-Based Strain-Aware Metagenome Assembly”, Frontiers in Genetics, vol. 13, 2022, : 868280.
Luo, X., Kang, X., Schönhuth, A.: Enhancing Long-Read-Based Strain-Aware Metagenome Assembly. Frontiers in Genetics. 13, : 868280 (2022).
Luo, Xiao, Kang, Xiangbin, and Schönhuth, Alexander. “Enhancing Long-Read-Based Strain-Aware Metagenome Assembly”. Frontiers in Genetics 13 (2022): 868280.
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