期刊
FRONTIERS IN ECOLOGY AND EVOLUTION
卷 8, 期 -, 页码 -出版社
FRONTIERS MEDIA SA
DOI: 10.3389/fevo.2020.00084
关键词
ancient DNA; BLAST; MEGAN; metagenomics; sedaDNA; taxonomic assignment
类别
资金
- European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme (ERC) [670518]
- European Research Council (ERC) [670518] Funding Source: European Research Council (ERC)
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.
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