Assessment of metagenomic assembly using simulated next generation sequencing data.

Due to the complexity of the protocols and a limited knowledge of the nature of microbial communities, simulating metagenomic sequences plays an important role in testing the performance of existing tools and data analysis methods with metagenomic data. We developed metagenomic read simulators with...

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Autores principales:	Daniel R Mende, Alison S Waller, Shinichi Sunagawa, Aino I Järvelin, Michelle M Chan, Manimozhiyan Arumugam, Jeroen Raes, Peer Bork
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b0b0ef110d5a498db462510b84130a34
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spelling	oai:doaj.org-article:b0b0ef110d5a498db462510b84130a342021-11-18T07:26:57ZAssessment of metagenomic assembly using simulated next generation sequencing data.1932-620310.1371/journal.pone.0031386https://doaj.org/article/b0b0ef110d5a498db462510b84130a342012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22384016/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Due to the complexity of the protocols and a limited knowledge of the nature of microbial communities, simulating metagenomic sequences plays an important role in testing the performance of existing tools and data analysis methods with metagenomic data. We developed metagenomic read simulators with platform-specific (Sanger, pyrosequencing, Illumina) base-error models, and simulated metagenomes of differing community complexities. We first evaluated the effect of rigorous quality control on Illumina data. Although quality filtering removed a large proportion of the data, it greatly improved the accuracy and contig lengths of resulting assemblies. We then compared the quality-trimmed Illumina assemblies to those from Sanger and pyrosequencing. For the simple community (10 genomes) all sequencing technologies assembled a similar amount and accurately represented the expected functional composition. For the more complex community (100 genomes) Illumina produced the best assemblies and more correctly resembled the expected functional composition. For the most complex community (400 genomes) there was very little assembly of reads from any sequencing technology. However, due to the longer read length the Sanger reads still represented the overall functional composition reasonably well. We further examined the effect of scaffolding of contigs using paired-end Illumina reads. It dramatically increased contig lengths of the simple community and yielded minor improvements to the more complex communities. Although the increase in contig length was accompanied by increased chimericity, it resulted in more complete genes and a better characterization of the functional repertoire. The metagenomic simulators developed for this research are freely available.Daniel R MendeAlison S WallerShinichi SunagawaAino I JärvelinMichelle M ChanManimozhiyan ArumugamJeroen RaesPeer BorkPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 2, p e31386 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Daniel R Mende Alison S Waller Shinichi Sunagawa Aino I Järvelin Michelle M Chan Manimozhiyan Arumugam Jeroen Raes Peer Bork Assessment of metagenomic assembly using simulated next generation sequencing data.
description	Due to the complexity of the protocols and a limited knowledge of the nature of microbial communities, simulating metagenomic sequences plays an important role in testing the performance of existing tools and data analysis methods with metagenomic data. We developed metagenomic read simulators with platform-specific (Sanger, pyrosequencing, Illumina) base-error models, and simulated metagenomes of differing community complexities. We first evaluated the effect of rigorous quality control on Illumina data. Although quality filtering removed a large proportion of the data, it greatly improved the accuracy and contig lengths of resulting assemblies. We then compared the quality-trimmed Illumina assemblies to those from Sanger and pyrosequencing. For the simple community (10 genomes) all sequencing technologies assembled a similar amount and accurately represented the expected functional composition. For the more complex community (100 genomes) Illumina produced the best assemblies and more correctly resembled the expected functional composition. For the most complex community (400 genomes) there was very little assembly of reads from any sequencing technology. However, due to the longer read length the Sanger reads still represented the overall functional composition reasonably well. We further examined the effect of scaffolding of contigs using paired-end Illumina reads. It dramatically increased contig lengths of the simple community and yielded minor improvements to the more complex communities. Although the increase in contig length was accompanied by increased chimericity, it resulted in more complete genes and a better characterization of the functional repertoire. The metagenomic simulators developed for this research are freely available.
format	article
author	Daniel R Mende Alison S Waller Shinichi Sunagawa Aino I Järvelin Michelle M Chan Manimozhiyan Arumugam Jeroen Raes Peer Bork
author_facet	Daniel R Mende Alison S Waller Shinichi Sunagawa Aino I Järvelin Michelle M Chan Manimozhiyan Arumugam Jeroen Raes Peer Bork
author_sort	Daniel R Mende
title	Assessment of metagenomic assembly using simulated next generation sequencing data.
title_short	Assessment of metagenomic assembly using simulated next generation sequencing data.
title_full	Assessment of metagenomic assembly using simulated next generation sequencing data.
title_fullStr	Assessment of metagenomic assembly using simulated next generation sequencing data.
title_full_unstemmed	Assessment of metagenomic assembly using simulated next generation sequencing data.
title_sort	assessment of metagenomic assembly using simulated next generation sequencing data.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/b0b0ef110d5a498db462510b84130a34
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Assessment of metagenomic assembly using simulated next generation sequencing data.

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