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2020-04-24Zeitschriftenartikel
Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A
dc.contributor.authorDavid, Laurent
dc.contributor.authorVicedomini, Riccardo
dc.contributor.authorRichard, Hugues
dc.contributor.authorCarbone, Alessandro
dc.date.accessioned2024-02-08T10:44:16Z
dc.date.available2024-02-08T10:44:16Z
dc.date.issued2020-04-24none
dc.identifier.other10.1093/bioinformatics/btaa272
dc.identifier.urihttp://edoc.rki.de/176904/11486
dc.description.abstractMotivation The understanding of the ever-increasing number of metagenomic sequences accumulating in our databases demands for approaches that rapidly ‘explore’ the content of multiple and/or large metagenomic datasets with respect to specific domain targets, avoiding full domain annotation and full assembly. Results S3A is a fast and accurate domain-targeted assembler designed for a rapid functional profiling. It is based on a novel construction and a fast traversal of the Overlap-Layout-Consensus graph, designed to reconstruct coding regions from domain annotated metagenomic sequence reads. S3A relies on high-quality domain annotation to efficiently assemble metagenomic sequences and on the design of a new confidence measure for a fast evaluation of overlapping reads. Its implementation is highly generic and can be applied to any arbitrary type of annotation. On simulated data, S3A achieves a level of accuracy similar to that of classical metagenomics assembly tools while permitting to conduct a faster and sensitive profiling on domains of interest. When studying a few dozens of functional domains—a typical scenario—S3A is up to an order of magnitude faster than general purpose metagenomic assemblers, thus enabling the analysis of a larger number of datasets in the same amount of time. S3A opens new avenues to the fast exploration of the rapidly increasing number of metagenomic datasets displaying an ever-increasing size.eng
dc.language.isoengnone
dc.publisherRobert Koch-Institut
dc.rights(CC BY-NC 3.0 DE) Namensnennung - Nicht kommerziell 3.0 Deutschlandger
dc.rights.urihttp://creativecommons.org/licenses/by-nc/3.0/de/
dc.subjectalgorithmseng
dc.subjectmetagenomeeng
dc.subjectmetagenomicseng
dc.subjectsequence analysiseng
dc.subjectsoftwareeng
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titleTargeted domain assembly for fast functional profiling of metagenomic datasets with S3Anone
dc.typearticle
dc.identifier.urnurn:nbn:de:0257-176904/11486-2
dc.type.versionpublishedVersionnone
local.edoc.container-titleBioinformaticsnone
local.edoc.container-issn1367-4811none
local.edoc.pages7none
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://academic.oup.com/bioinformaticsnone
local.edoc.container-publisher-nameOxford University Pressnone
local.edoc.container-volume36none
local.edoc.container-issue13none
local.edoc.container-reportyear2020none
local.edoc.container-firstpage3975none
local.edoc.container-lastpage3981none
dc.description.versionPeer Reviewednone

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