Metagenomic Data Assembly - The Way of Decoding Unknown Microorganisms

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2021 Apr 9

PMID 33833738

Citations 46

Authors

Alla L Lapidus

Anton I Korobeynikov

Affiliations

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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.

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References

Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P . A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev. 2008; 72(4):557-78, Table of Contents. PMC: 2593568. DOI: 10.1128/MMBR.00009-08. View

Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J . Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol. 2012; 13(12):R122. PMC: 4056372. DOI: 10.1186/gb-2012-13-12-r122. View

Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapidus A . Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol. 2013; 20(10):714-37. PMC: 3791033. DOI: 10.1089/cmb.2013.0084. View

Uritskiy G, DiRuggiero J, Taylor J . MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome. 2018; 6(1):158. PMC: 6138922. DOI: 10.1186/s40168-018-0541-1. View

Wick R, Schultz M, Zobel J, Holt K . Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 2015; 31(20):3350-2. PMC: 4595904. DOI: 10.1093/bioinformatics/btv383. View

Mallawaarachchi V, Wickramarachchi A, Lin Y . GraphBin: refined binning of metagenomic contigs using assembly graphs. Bioinformatics. 2020; 36(11):3307-3313. DOI: 10.1093/bioinformatics/btaa180. View

Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A, Pevzner P . plasmidSPAdes: assembling plasmids from whole genome sequencing data. Bioinformatics. 2016; 32(22):3380-3387. DOI: 10.1093/bioinformatics/btw493. View

Pellow D, Zorea A, Probst M, Furman O, Segal A, Mizrahi I . SCAPP: an algorithm for improved plasmid assembly in metagenomes. Microbiome. 2021; 9(1):144. PMC: 8228940. DOI: 10.1186/s40168-021-01068-z. View

Clarke E, Taylor L, Zhao C, Connell A, Lee J, Fett B . Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments. Microbiome. 2019; 7(1):46. PMC: 6429786. DOI: 10.1186/s40168-019-0658-x. View

10.

Bushmanova E, Antipov D, Lapidus A, Prjibelski A . rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. Gigascience. 2019; 8(9). PMC: 6736328. DOI: 10.1093/gigascience/giz100. View

11.

Ayling M, Clark M, Leggett R . New approaches for metagenome assembly with short reads. Brief Bioinform. 2019; 21(2):584-594. PMC: 7299287. DOI: 10.1093/bib/bbz020. View

12.

Lang D, Zhang S, Ren P, Liang F, Sun Z, Meng G . Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore. Gigascience. 2020; 9(12). PMC: 7736813. DOI: 10.1093/gigascience/giaa123. View

13.

Prjibelski A, Vasilinetc I, Bankevich A, Gurevich A, Krivosheeva T, Nurk S . ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics. 2014; 30(12):i293-301. PMC: 4058921. DOI: 10.1093/bioinformatics/btu266. View

14.

Fuks G, Elgart M, Amir A, Zeisel A, Turnbaugh P, Soen Y . Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling. Microbiome. 2018; 6(1):17. PMC: 5787238. DOI: 10.1186/s40168-017-0396-x. View

15.

Menzel P, Ng K, Krogh A . Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun. 2016; 7:11257. PMC: 4833860. DOI: 10.1038/ncomms11257. View

16.

Antipov D, Raiko M, Lapidus A, Pevzner P . Plasmid detection and assembly in genomic and metagenomic data sets. Genome Res. 2019; 29(6):961-968. PMC: 6581055. DOI: 10.1101/gr.241299.118. View

17.

Antipov D, Korobeynikov A, McLean J, Pevzner P . hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics. 2015; 32(7):1009-15. PMC: 4907386. DOI: 10.1093/bioinformatics/btv688. View

18.

Bushnell B, Rood J, Singer E . BBMerge - Accurate paired shotgun read merging via overlap. PLoS One. 2017; 12(10):e0185056. PMC: 5657622. DOI: 10.1371/journal.pone.0185056. View

19.

Treangen T, Koren S, Sommer D, Liu B, Astrovskaya I, Ondov B . MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol. 2013; 14(1):R2. PMC: 4053804. DOI: 10.1186/gb-2013-14-1-r2. View

20.

Song W, Thomas T . Binning_refiner: improving genome bins through the combination of different binning programs. Bioinformatics. 2017; 33(12):1873-1875. DOI: 10.1093/bioinformatics/btx086. View