Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.

Next generation sequencing (NGS) of metagenomic samples is becoming a standard approach to detect individual species or pathogenic strains of microorganisms. Computer programs used in the NGS community have to balance between speed and sensitivity and as a result, species or strain level identificat...

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Autores principales:	Lőrinc S Pongor, Roberto Vera, Balázs Ligeti
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/61c68f04868048e1ae46cf9d57e56620
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spelling	oai:doaj.org-article:61c68f04868048e1ae46cf9d57e566202021-11-25T06:06:35ZFast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.1932-620310.1371/journal.pone.0103441https://doaj.org/article/61c68f04868048e1ae46cf9d57e566202014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25077800/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Next generation sequencing (NGS) of metagenomic samples is becoming a standard approach to detect individual species or pathogenic strains of microorganisms. Computer programs used in the NGS community have to balance between speed and sensitivity and as a result, species or strain level identification is often inaccurate and low abundance pathogens can sometimes be missed. We have developed Taxoner, an open source, taxon assignment pipeline that includes a fast aligner (e.g. Bowtie2) and a comprehensive DNA sequence database. We tested the program on simulated datasets as well as experimental data from Illumina, IonTorrent, and Roche 454 sequencing platforms. We found that Taxoner performs as well as, and often better than BLAST, but requires two orders of magnitude less running time meaning that it can be run on desktop or laptop computers. Taxoner is slower than the approaches that use small marker databases but is more sensitive due the comprehensive reference database. In addition, it can be easily tuned to specific applications using small tailored databases. When applied to metagenomic datasets, Taxoner can provide a functional summary of the genes mapped and can provide strain level identification. Taxoner is written in C for Linux operating systems. The code and documentation are available for research applications at http://code.google.com/p/taxoner.Lőrinc S PongorRoberto VeraBalázs LigetiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 7, p e103441 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Lőrinc S Pongor Roberto Vera Balázs Ligeti Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.
description	Next generation sequencing (NGS) of metagenomic samples is becoming a standard approach to detect individual species or pathogenic strains of microorganisms. Computer programs used in the NGS community have to balance between speed and sensitivity and as a result, species or strain level identification is often inaccurate and low abundance pathogens can sometimes be missed. We have developed Taxoner, an open source, taxon assignment pipeline that includes a fast aligner (e.g. Bowtie2) and a comprehensive DNA sequence database. We tested the program on simulated datasets as well as experimental data from Illumina, IonTorrent, and Roche 454 sequencing platforms. We found that Taxoner performs as well as, and often better than BLAST, but requires two orders of magnitude less running time meaning that it can be run on desktop or laptop computers. Taxoner is slower than the approaches that use small marker databases but is more sensitive due the comprehensive reference database. In addition, it can be easily tuned to specific applications using small tailored databases. When applied to metagenomic datasets, Taxoner can provide a functional summary of the genes mapped and can provide strain level identification. Taxoner is written in C for Linux operating systems. The code and documentation are available for research applications at http://code.google.com/p/taxoner.
format	article
author	Lőrinc S Pongor Roberto Vera Balázs Ligeti
author_facet	Lőrinc S Pongor Roberto Vera Balázs Ligeti
author_sort	Lőrinc S Pongor
title	Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.
title_short	Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.
title_full	Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.
title_fullStr	Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.
title_full_unstemmed	Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.
title_sort	fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop pc: application to metagenomic datasets and pathogen identification.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/61c68f04868048e1ae46cf9d57e56620
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Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.

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