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PIA : more accurate taxonomic assignment of metagenomic data demonstrated on sedaDNA from the North sea
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Cribdon, Becky, Ware, Roselyn, Smith, Oliver, Gaffney, Vincent and Allaby, Robin G. (2020) PIA : more accurate taxonomic assignment of metagenomic data demonstrated on sedaDNA from the North sea. Frontiers in Ecology and Evolution, 8 . 84. doi:10.3389/fevo.2020.00084 ISSN 2296-701X.
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Official URL: https://doi.org/10.3389/fevo.2020.00084
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.
| Item Type: | Journal Article | ||||||
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| Subjects: | Q Science > QH Natural history Q Science > QP Physiology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||
| SWORD Depositor: | Library Publications Router | ||||||
| Library of Congress Subject Headings (LCSH): | Metagenomics , DNA, Fossil , Biology -- Classification, Computational biology | ||||||
| Journal or Publication Title: | Frontiers in Ecology and Evolution | ||||||
| Publisher: | Frontiers Media | ||||||
| ISSN: | 2296-701X | ||||||
| Official Date: | 3 April 2020 | ||||||
| Dates: |
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| Volume: | 8 | ||||||
| Article Number: | 84 | ||||||
| DOI: | 10.3389/fevo.2020.00084 | ||||||
| Status: | Peer Reviewed | ||||||
| Publication Status: | Published | ||||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||||
| Date of first compliant deposit: | 21 April 2020 | ||||||
| Date of first compliant Open Access: | 21 April 2020 | ||||||
| RIOXX Funder/Project Grant: |
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