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dc.contributor.authorGaffney, Vincent L.
dc.contributor.authorCribdon, B.
dc.contributor.authorWare, R.
dc.contributor.authorSmith, O.
dc.contributor.authorAllaby, R.
dc.date.accessioned2020-06-26T13:05:44Z
dc.date.available2020-06-26T13:05:44Z
dc.date.issued2020-04-03
dc.identifier.citationCribdon B, Ware R, Smith O et al (2020) PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Sea. Frontiers in Ecology and Evolution.en_US
dc.identifier.urihttp://hdl.handle.net/10454/17876
dc.descriptionYesen_US
dc.description.abstractAssigning metagenomic reads to taxa presents significant challenges. Existing approaches address some issues, but are mostly limited to metabarcoding or optimized for microbial data. We present PIA (Phylogenetic Intersection Analysis): a taxonomic binner that works from standard BLAST output while mitigating key effects of incomplete databases. Benchmarking against MEGAN using sedaDNA suggests that, while PIA is less sensitive, it can be more accurate. We use known sequences to estimate the accuracy of PIA at up to 96% when the real organism is not represented in the database. For ancient DNA, where taxa of interest are frequently over-represented domesticates or absent, poorly-known organisms, more accurate assignment is critical, even at the expense of sensitivity. PIA offers an approach to objectively filter out false positive hits without the need to manually remove taxa and so make presuppositions about past environments and their palaeoecologies.en_US
dc.description.sponsorshipEuropean Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (ERC funded project no. 670518 LOST FRONTIERen_US
dc.language.isoenen_US
dc.relation.isreferencedbyhttps://doi.org/10.3389/fevo.2020.00084en_US
dc.rights(c) 2020 The Authors. This is an Open Access article distributed under the Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0/)en_US
dc.subjectPIAen_US
dc.subjectDNAen_US
dc.subjectMetagenomicsen_US
dc.titlePIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Seaen_US
dc.status.refereedYesen_US
dc.typeArticleen_US
dc.type.versionPublished versionen_US
refterms.dateFOA2020-06-26T13:06:12Z


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