Benchmarking different approaches for Norovirus genome assembly in metagenome samples

Abstract Background Genome assembly of viruses with high mutation rates, such as Norovirus and other RNA viruses, or from metagenome samples, poses a challenge for the scientific community due to the coexistence of several viral quasispecies and strains. Furthermore, there is no standard method for...

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Autores principales:	Azahara Fuentes-Trillo, Carolina Monzó, Iris Manzano, Cristina Santiso-Bellón, Juliana da Silva Ribeiro de Andrade, Roberto Gozalbo-Rovira, Ana-Bárbara García-García, Jesús Rodríguez-Díaz, Felipe Javier Chaves
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Norovirus Genome de-novo assembly Metagenomics Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/d27c4b42731d41e5a5c24552f2fedd12
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spelling	oai:doaj.org-article:d27c4b42731d41e5a5c24552f2fedd122021-11-28T12:23:09ZBenchmarking different approaches for Norovirus genome assembly in metagenome samples10.1186/s12864-021-08067-21471-2164https://doaj.org/article/d27c4b42731d41e5a5c24552f2fedd122021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08067-2https://doaj.org/toc/1471-2164Abstract Background Genome assembly of viruses with high mutation rates, such as Norovirus and other RNA viruses, or from metagenome samples, poses a challenge for the scientific community due to the coexistence of several viral quasispecies and strains. Furthermore, there is no standard method for obtaining whole-genome sequences in non-related patients. After polyA RNA isolation and sequencing in eight patients with acute gastroenteritis, we evaluated two de Bruijn graph assemblers (SPAdes and MEGAHIT), combined with four different and common pre-assembly strategies, and compared those yielding whole genome Norovirus contigs. Results Reference-genome guided strategies with both host and target virus did not present any advantages compared to the assembly of non-filtered data in the case of SPAdes, and in the case of MEGAHIT, only host genome filtering presented improvements. MEGAHIT performed better than SPAdes in most samples, reaching complete genome sequences in most of them for all the strategies employed. Read binning with CD-HIT improved assembly when paired with different analysis strategies, and more notably in the case of SPAdes. Conclusions Not all metagenome assemblies are equal and the choice in the workflow depends on the species studied and the prior steps to analysis. We may need different approaches even for samples treated equally due to the presence of high intra host variability. We tested and compared different workflows for the accurate assembly of Norovirus genomes and established their assembly capacities for this purpose.Azahara Fuentes-TrilloCarolina MonzóIris ManzanoCristina Santiso-BellónJuliana da Silva Ribeiro de AndradeRoberto Gozalbo-RoviraAna-Bárbara García-GarcíaJesús Rodríguez-DíazFelipe Javier ChavesBMCarticleNorovirusGenome de-novo assemblyMetagenomicsBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Norovirus Genome de-novo assembly Metagenomics Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Norovirus Genome de-novo assembly Metagenomics Biotechnology TP248.13-248.65 Genetics QH426-470 Azahara Fuentes-Trillo Carolina Monzó Iris Manzano Cristina Santiso-Bellón Juliana da Silva Ribeiro de Andrade Roberto Gozalbo-Rovira Ana-Bárbara García-García Jesús Rodríguez-Díaz Felipe Javier Chaves Benchmarking different approaches for Norovirus genome assembly in metagenome samples
description	Abstract Background Genome assembly of viruses with high mutation rates, such as Norovirus and other RNA viruses, or from metagenome samples, poses a challenge for the scientific community due to the coexistence of several viral quasispecies and strains. Furthermore, there is no standard method for obtaining whole-genome sequences in non-related patients. After polyA RNA isolation and sequencing in eight patients with acute gastroenteritis, we evaluated two de Bruijn graph assemblers (SPAdes and MEGAHIT), combined with four different and common pre-assembly strategies, and compared those yielding whole genome Norovirus contigs. Results Reference-genome guided strategies with both host and target virus did not present any advantages compared to the assembly of non-filtered data in the case of SPAdes, and in the case of MEGAHIT, only host genome filtering presented improvements. MEGAHIT performed better than SPAdes in most samples, reaching complete genome sequences in most of them for all the strategies employed. Read binning with CD-HIT improved assembly when paired with different analysis strategies, and more notably in the case of SPAdes. Conclusions Not all metagenome assemblies are equal and the choice in the workflow depends on the species studied and the prior steps to analysis. We may need different approaches even for samples treated equally due to the presence of high intra host variability. We tested and compared different workflows for the accurate assembly of Norovirus genomes and established their assembly capacities for this purpose.
format	article
author	Azahara Fuentes-Trillo Carolina Monzó Iris Manzano Cristina Santiso-Bellón Juliana da Silva Ribeiro de Andrade Roberto Gozalbo-Rovira Ana-Bárbara García-García Jesús Rodríguez-Díaz Felipe Javier Chaves
author_facet	Azahara Fuentes-Trillo Carolina Monzó Iris Manzano Cristina Santiso-Bellón Juliana da Silva Ribeiro de Andrade Roberto Gozalbo-Rovira Ana-Bárbara García-García Jesús Rodríguez-Díaz Felipe Javier Chaves
author_sort	Azahara Fuentes-Trillo
title	Benchmarking different approaches for Norovirus genome assembly in metagenome samples
title_short	Benchmarking different approaches for Norovirus genome assembly in metagenome samples
title_full	Benchmarking different approaches for Norovirus genome assembly in metagenome samples
title_fullStr	Benchmarking different approaches for Norovirus genome assembly in metagenome samples
title_full_unstemmed	Benchmarking different approaches for Norovirus genome assembly in metagenome samples
title_sort	benchmarking different approaches for norovirus genome assembly in metagenome samples
publisher	BMC
publishDate	2021
url	https://doaj.org/article/d27c4b42731d41e5a5c24552f2fedd12
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Benchmarking different approaches for Norovirus genome assembly in metagenome samples

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