ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.

Viral metagenomics, also known as virome studies, have yielded an unprecedented number of novel sequences, essential in recognizing and characterizing the etiological agent and the origin of emerging infectious diseases. Several tools and pipelines have been developed, to date, for the identificatio...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Nikolas Dovrolis, Katerina Kassela, Konstantinos Konstantinidis, Adamantia Kouvela, Stavroula Veletza, Ioannis Karakasiliotis
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/3a30a4f407604e0593af330a1fc53b10
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:3a30a4f407604e0593af330a1fc53b10
record_format	dspace
spelling	oai:doaj.org-article:3a30a4f407604e0593af330a1fc53b102021-12-02T19:58:07ZZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.1553-734X1553-735810.1371/journal.pcbi.1009304https://doaj.org/article/3a30a4f407604e0593af330a1fc53b102021-08-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009304https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Viral metagenomics, also known as virome studies, have yielded an unprecedented number of novel sequences, essential in recognizing and characterizing the etiological agent and the origin of emerging infectious diseases. Several tools and pipelines have been developed, to date, for the identification and assembly of viral genomes. Assembly pipelines often result in viral genomes contaminated with host genetic material, some of which are currently deposited into public databases. In the current report, we present a group of deposited sequences that encompass ribosomal RNA (rRNA) contamination. We highlight the detrimental role of chimeric next generation sequencing reads, between host rRNA sequences and viral sequences, in virus genome assembly and we present the hindrances these reads may pose to current methodologies. We have further developed a refining pipeline, the Zero Waste Algorithm (ZWA) that assists in the assembly of low abundance viral genomes. ZWA performs context-depended trimming of chimeric reads, precisely removing their rRNA moiety. These, otherwise discarded, reads were fed to the assembly pipeline and assisted in the construction of larger and cleaner contigs making a substantial impact on current assembly methodologies. ZWA pipeline may significantly enhance virus genome assembly from low abundance samples and virus metagenomics approaches in which a small number of reads determine genome quality and integrity.Nikolas DovrolisKaterina KasselaKonstantinos KonstantinidisAdamantia KouvelaStavroula VeletzaIoannis KarakasiliotisPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 8, p e1009304 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Nikolas Dovrolis Katerina Kassela Konstantinos Konstantinidis Adamantia Kouvela Stavroula Veletza Ioannis Karakasiliotis ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.
description	Viral metagenomics, also known as virome studies, have yielded an unprecedented number of novel sequences, essential in recognizing and characterizing the etiological agent and the origin of emerging infectious diseases. Several tools and pipelines have been developed, to date, for the identification and assembly of viral genomes. Assembly pipelines often result in viral genomes contaminated with host genetic material, some of which are currently deposited into public databases. In the current report, we present a group of deposited sequences that encompass ribosomal RNA (rRNA) contamination. We highlight the detrimental role of chimeric next generation sequencing reads, between host rRNA sequences and viral sequences, in virus genome assembly and we present the hindrances these reads may pose to current methodologies. We have further developed a refining pipeline, the Zero Waste Algorithm (ZWA) that assists in the assembly of low abundance viral genomes. ZWA performs context-depended trimming of chimeric reads, precisely removing their rRNA moiety. These, otherwise discarded, reads were fed to the assembly pipeline and assisted in the construction of larger and cleaner contigs making a substantial impact on current assembly methodologies. ZWA pipeline may significantly enhance virus genome assembly from low abundance samples and virus metagenomics approaches in which a small number of reads determine genome quality and integrity.
format	article
author	Nikolas Dovrolis Katerina Kassela Konstantinos Konstantinidis Adamantia Kouvela Stavroula Veletza Ioannis Karakasiliotis
author_facet	Nikolas Dovrolis Katerina Kassela Konstantinos Konstantinidis Adamantia Kouvela Stavroula Veletza Ioannis Karakasiliotis
author_sort	Nikolas Dovrolis
title	ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.
title_short	ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.
title_full	ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.
title_fullStr	ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.
title_full_unstemmed	ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.
title_sort	zwa: viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/3a30a4f407604e0593af330a1fc53b10
work_keys_str_mv	AT nikolasdovrolis zwaviralgenomeassemblyandcharacterizationhindrancesfromvirushostchimericreadsarefiningapproach AT katerinakassela zwaviralgenomeassemblyandcharacterizationhindrancesfromvirushostchimericreadsarefiningapproach AT konstantinoskonstantinidis zwaviralgenomeassemblyandcharacterizationhindrancesfromvirushostchimericreadsarefiningapproach AT adamantiakouvela zwaviralgenomeassemblyandcharacterizationhindrancesfromvirushostchimericreadsarefiningapproach AT stavroulaveletza zwaviralgenomeassemblyandcharacterizationhindrancesfromvirushostchimericreadsarefiningapproach AT ioanniskarakasiliotis zwaviralgenomeassemblyandcharacterizationhindrancesfromvirushostchimericreadsarefiningapproach
_version_	1718375770615709696

ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.

Ejemplares similares