ArticleBioinformatics (Oxford, England)2022
Tiara: deep learning-based classification system for eukaryotic sequences.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers, 1 of them a synthesis that pooled it.
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Who cites it
82 citing papers in PubMed, 1 synthesis or guideline pooled it, 124 citations in OpenAlex.
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- ntStat: k-mer characterization using occurrence statistics in raw sequencing data.PLoS computational biology · 2026Article
- ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.Molecular ecology resources · 2026Article
- Unveiling the biodiversity of large DNA viruses in intertidal mudflats via metagenomics.Nature communications · 2026Article
- Single-cell sequencing reveals unexpected genetic diversity amongMicrobial genomics · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Metabarcoding and metagenomic data across aquatic environmental gradients along the coasts of France and Chile.Scientific data · 2026Article
- Euglenid Extrachromosomal DNA: Assembly and Annotation.Methods in molecular biology (Clifton, N.J.) · 2026Article
22 more citing papers are in PubMed but not listed here.
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3 authors at 1 institution in 1 country.
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Abstract
motivationWith a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of eukaryotic diversity.
resultsWe developed Tiara, a deep-learning-based approach for the identification of eukaryotic sequences in the metagenomic datasets. Its two-step classification process enables the classification of nuclear and organellar eukaryotic fractions and subsequently divides organellar sequences into plastidial and mitochondrial. Using the test dataset, we have shown that Tiara performed similarly to EukRep for prokaryotes classification and outperformed it for eukaryotes classification with lower calculation time. In the tests on the real data, Tiara performed better than EukRep in analyzing the small dataset representing eukaryotic cell microbiome and large dataset from the pelagic zone of oceans. Tiara is also the only available tool correctly classifying organellar sequences, which was confirmed by the recovery of nearly complete plastid and mitochondrial genomes from the test data and real metagenomic data. AVAILABILITY AND IMPLEMENTATION: Tiara is implemented in python 3.8, available at https://github.com/ibe-uw/tiara and tested on Unix-based systems. It is released under an open-source MIT license and documentation is available at https://ibe-uw.github.io/tiara. Version 1.0.1 of Tiara has been used for all benchmarks. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.