PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Sea
| Autor: | Vincent Gaffney, Becky Cribdon, Oliver Smith, Roselyn Ware, Robin G. Allaby |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine Computer science lcsh:Evolution computer.software_genre 010603 evolutionary biology 01 natural sciences taxonomic assignment 03 medical and health sciences lcsh:QH540-549.5 lcsh:QH359-425 sedaDNA BLAST North sea ancient DNA Ecology Evolution Behavior and Systematics Organism metagenomics Ecology Phylogenetic tree QH QP 030104 developmental biology Taxon Ancient DNA Metagenomics MEGAN lcsh:Ecology Data mining computer |
| Zdroj: | Frontiers in Ecology and Evolution, Vol 8 (2020) Frontiers in Ecology and Evolution |
| ISSN: | 2296-701X |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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