Metagenomic Data Assembly – The Way of Decoding Unknown Microorganisms

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Metagenomic Data Assembly – The Way of Decoding Unknown Microorganisms. / Lapidus, Alla L.; Korobeynikov, Anton I.

In: Frontiers in Microbiology, Vol. 12, 613791, 23.03.2021.

Research output: Contribution to journal › Review article › peer-review

BibTeX

@article{63464e2bb86641adbd6f3f965124c79b,

title = "Metagenomic Data Assembly – The Way of Decoding Unknown Microorganisms",

abstract = "Metagenomics is a segment of conventional microbial genomics dedicated to the sequencing and analysis of combined genomic DNA of entire environmental samples. The most critical step of the metagenomic data analysis is the reconstruction of individual genes and genomes of the microorganisms in the communities using metagenomic assemblers – computational programs that put together small fragments of sequenced DNA generated by sequencing instruments. Here, we describe the challenges of metagenomic assembly, a wide spectrum of applications in which metagenomic assemblies were used to better understand the ecology and evolution of microbial ecosystems, and present one of the most efficient microbial assemblers, SPAdes that was upgraded to become applicable for metagenomics.",

keywords = "Metagenomics, Microbiota, Microbiome, Genome assembly, SPAdes, algorithms, metagenomic assembly, metagenomics, microbiota",

author = "Lapidus, {Alla L.} and Korobeynikov, {Anton I.}",

year = "2021",

month = mar,

day = "23",

doi = "10.3389/fmicb.2021.613791",

language = "English",

volume = "12",

journal = "Frontiers in Microbiology",

issn = "1664-302X",

publisher = "Frontiers Media S.A.",

}

RIS

TY - JOUR

T1 - Metagenomic Data Assembly – The Way of Decoding Unknown Microorganisms

AU - Lapidus, Alla L.

AU - Korobeynikov, Anton I.

PY - 2021/3/23

Y1 - 2021/3/23

N2 - Metagenomics is a segment of conventional microbial genomics dedicated to the sequencing and analysis of combined genomic DNA of entire environmental samples. The most critical step of the metagenomic data analysis is the reconstruction of individual genes and genomes of the microorganisms in the communities using metagenomic assemblers – computational programs that put together small fragments of sequenced DNA generated by sequencing instruments. Here, we describe the challenges of metagenomic assembly, a wide spectrum of applications in which metagenomic assemblies were used to better understand the ecology and evolution of microbial ecosystems, and present one of the most efficient microbial assemblers, SPAdes that was upgraded to become applicable for metagenomics.

AB - Metagenomics is a segment of conventional microbial genomics dedicated to the sequencing and analysis of combined genomic DNA of entire environmental samples. The most critical step of the metagenomic data analysis is the reconstruction of individual genes and genomes of the microorganisms in the communities using metagenomic assemblers – computational programs that put together small fragments of sequenced DNA generated by sequencing instruments. Here, we describe the challenges of metagenomic assembly, a wide spectrum of applications in which metagenomic assemblies were used to better understand the ecology and evolution of microbial ecosystems, and present one of the most efficient microbial assemblers, SPAdes that was upgraded to become applicable for metagenomics.

KW - Metagenomics

KW - Microbiota

KW - Microbiome

KW - Genome assembly

KW - SPAdes

KW - algorithms

KW - metagenomic assembly

KW - metagenomics

KW - microbiota

UR - http://www.scopus.com/inward/record.url?scp=85103782072&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/460de301-6420-3565-b061-4ccfd01d39fc/

U2 - 10.3389/fmicb.2021.613791

DO - 10.3389/fmicb.2021.613791

M3 - Review article

AN - SCOPUS:85103782072

VL - 12

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

M1 - 613791

ER -

ID: 75242360