Strategies and Tools in illumina & Nanopore - integrated metagenomic analysis of microbiome data.

Xia, Yu1,2,3; Li, Xiang1; Wu, Ziqi1; Nie, Cailong1; Cheng, Zhanwen1; Sun, Yuhong1; Liu, Lei4; Zhang, Tong4

2023-01-09

10.1002/imt2.72

iMeta   影响因子和分区

2770-5986

2770-596X

["Metagenomic strategy serves as the foundation for the ecological exploration of novel bioresources (e.g., industrial enzymes and bioactive molecules) and biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. Recent advancements in sequencing technology have fostered rapid development in the field of microbiome research where an increasing number of studies have applied both illumina short reads (SRs) and nanopore long reads (LRs) sequencing in their metagenomic workflow. However, given the high complexity of an environmental microbiome data set and the bioinformatic challenges caused by the unique features of these sequencing technologies, integrating SRs and LRs is not as straightforward as one might assume. The fast renewal of existing tools and growing diversity of new algorithms make access to this field even more difficult. Therefore, here we systematically summarized the complete workflow from DNA extraction to data processing strategies for applying illumina and nanopore-integrated metagenomics in the investigation in environmental microbiomes. Overall, this review aims to provide a timely knowledge framework for researchers that are interested in or are struggling with the SRs and LRs integration in their metagenomic analysis. The discussions presented will facilitate improved ecological understanding of community functionalities and assembly of natural, engineered, and human microbiomes, benefiting researchers from multiple disciplines.","Strategies and tools in illumina and nanopore-integrated metagenomic analysis of microbiome data.image","A timely knowledge framework to integrate nanopore long reads and illumina short reads is provided.Workflow of common strategies for illumina and nanopore integration is illustrated in Figure 1.Algorithm basis and application properties of tools are summarized in Table 3."]

gene-centric metagenomics genome-centric metagenomics hybrid sequencing illumina and nanopore-integrated metagenomics microbiome metagenomics nanopore sequencing

ESCI

英语

第一 ; 通讯

National Key Research and Development Program of China[2022YFE0103200] ; null[42007216] ; null[42177357] ; null[42277103]

Microbiology

Microbiology

WOS:001136693100001

WILEY

人工提交

1.School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, China
2.State Environmental Protection KeyLaboratory of Integrated Surface Water‐Groundwater Pollution Control, School ofEnvironmental Science and Engineering,Southern University of Science andTechnology, Shenzhen, China
3.Guangdong Provincial Key Laboratory ofSoil and Groundwater Pollution Control,School of Environmental Science andEngineering, Southern University ofScience and Technology, Shenzhen, China
4.Environmental Microbiome Engineeringand Biotechnology Laboratory, TheUniversity of Hong Kong, Hong KongSAR, China

Xia, Yu,Li, Xiang,Wu, Ziqi,et al. Strategies and Tools in illumina & Nanopore - integrated metagenomic analysis of microbiome data.[J]. iMeta,2023,2(1).

Xia, Yu.,Li, Xiang.,Wu, Ziqi.,Nie, Cailong.,Cheng, Zhanwen.,...&Zhang, Tong.(2023).Strategies and Tools in illumina & Nanopore - integrated metagenomic analysis of microbiome data..iMeta,2(1).

Xia, Yu,et al."Strategies and Tools in illumina & Nanopore - integrated metagenomic analysis of microbiome data.".iMeta 2.1(2023).