A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data
Metagenomic sequencing provides a culture-independent avenue to investigate the complex microbial communities by constructing metagenome-assembled genomes (MAGs). A MAG represents a microbial genome by a group of sequences from genome assembly with similar characteristics. It enables us to identify...
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2021
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oai:doaj.org-article:81ce4bd79f794535aef3ef13886c930b2021-12-02T05:00:24ZA review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data2001-037010.1016/j.csbj.2021.11.028https://doaj.org/article/81ce4bd79f794535aef3ef13886c930b2021-01-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2001037021004931https://doaj.org/toc/2001-0370Metagenomic sequencing provides a culture-independent avenue to investigate the complex microbial communities by constructing metagenome-assembled genomes (MAGs). A MAG represents a microbial genome by a group of sequences from genome assembly with similar characteristics. It enables us to identify novel species and understand their potential functions in a dynamic ecosystem. Many computational tools have been developed to construct and annotate MAGs from metagenomic sequencing, however, there is a prominent gap to comprehensively introduce their background and practical performance. In this paper, we have thoroughly investigated the computational tools designed for both upstream and downstream analyses, including metagenome assembly, metagenome binning, gene prediction, functional annotation, taxonomic classification, and profiling. We have categorized the commonly used tools into unique groups based on their functional background and introduced the underlying core algorithms and associated information to demonstrate a comparative outlook. Furthermore, we have emphasized the computational requisition and offered guidance to the users to select the most efficient tools. Finally, we have indicated current limitations, potential solutions, and future perspectives for further improving the tools of MAG construction and annotation. We believe that our work provides a consolidated resource for the current stage of MAG studies and shed light on the future development of more effective MAG analysis tools on metagenomic sequencing.Chao YangDebajyoti ChowdhuryZhenmiao ZhangWilliam K. CheungAiping LuZhaoxiang BianLu ZhangElsevierarticleMetagenomic sequencingMetagenome-assembled genomesGenome assemblyMetagenome binningGene predictionGene functional annotationBiotechnologyTP248.13-248.65ENComputational and Structural Biotechnology Journal, Vol 19, Iss , Pp 6301-6314 (2021) |
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DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Metagenomic sequencing Metagenome-assembled genomes Genome assembly Metagenome binning Gene prediction Gene functional annotation Biotechnology TP248.13-248.65 |
| spellingShingle |
Metagenomic sequencing Metagenome-assembled genomes Genome assembly Metagenome binning Gene prediction Gene functional annotation Biotechnology TP248.13-248.65 Chao Yang Debajyoti Chowdhury Zhenmiao Zhang William K. Cheung Aiping Lu Zhaoxiang Bian Lu Zhang A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data |
| description |
Metagenomic sequencing provides a culture-independent avenue to investigate the complex microbial communities by constructing metagenome-assembled genomes (MAGs). A MAG represents a microbial genome by a group of sequences from genome assembly with similar characteristics. It enables us to identify novel species and understand their potential functions in a dynamic ecosystem. Many computational tools have been developed to construct and annotate MAGs from metagenomic sequencing, however, there is a prominent gap to comprehensively introduce their background and practical performance. In this paper, we have thoroughly investigated the computational tools designed for both upstream and downstream analyses, including metagenome assembly, metagenome binning, gene prediction, functional annotation, taxonomic classification, and profiling. We have categorized the commonly used tools into unique groups based on their functional background and introduced the underlying core algorithms and associated information to demonstrate a comparative outlook. Furthermore, we have emphasized the computational requisition and offered guidance to the users to select the most efficient tools. Finally, we have indicated current limitations, potential solutions, and future perspectives for further improving the tools of MAG construction and annotation. We believe that our work provides a consolidated resource for the current stage of MAG studies and shed light on the future development of more effective MAG analysis tools on metagenomic sequencing. |
| format |
article |
| author |
Chao Yang Debajyoti Chowdhury Zhenmiao Zhang William K. Cheung Aiping Lu Zhaoxiang Bian Lu Zhang |
| author_facet |
Chao Yang Debajyoti Chowdhury Zhenmiao Zhang William K. Cheung Aiping Lu Zhaoxiang Bian Lu Zhang |
| author_sort |
Chao Yang |
| title |
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data |
| title_short |
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data |
| title_full |
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data |
| title_fullStr |
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data |
| title_full_unstemmed |
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data |
| title_sort |
review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data |
| publisher |
Elsevier |
| publishDate |
2021 |
| url |
https://doaj.org/article/81ce4bd79f794535aef3ef13886c930b |
| work_keys_str_mv |
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