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    PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Sea

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    Publication date
    2020-04-03
    Author
    Cribdon, B.
    Ware, R.
    Smith, O.
    Gaffney, Vincent L.
    Allaby, R.G.
    Keyword
    PIA
    DNA
    Metagenomics
    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/)
    Peer-Reviewed
    Yes
    
    Metadata
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    Abstract
    Assigning 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.
    URI
    http://hdl.handle.net/10454/17876
    Version
    Published version
    Citation
    Cribdon 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.
    Link to publisher’s version
    https://doi.org/10.3389/fevo.2020.00084
    Type
    Article
    Collections
    Life Sciences Publications

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