ArticleBioinformatics (Oxford, England)2017
PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater.Microbiology spectrum · 2024Article
- The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes.Animal microbiome · 2023Article
- Metagenome-assembled genomes indicate that antimicrobial resistance genes are highly prevalent among urban bacteria and multidrug and glycopeptide resistances are ubiquitous in most taxa.Frontiers in microbiology · 2023Article
- MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes.Environmental microbiome · 2022Article
- How Metagenomics Has Transformed Our Understanding of Bacteriophages in Microbiome Research.Microorganisms · 2022Review
- Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria.Water research X · 2021Article
- Article
- HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes.Nucleic acids research · 2021Article
- Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions.Cell host & microbe · 2020Article
- Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome.Gut microbes · 2020Article
- Experimental support for multidrug resistance transfer potential in the preterm infant gut microbiota.Pediatric research · 2020Observational
- Article
- TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.Nucleic acids research · 2020Article
- PHANOTATE: a novel approach to gene identification in phage genomes.Bioinformatics (Oxford, England) · 2019Article
- Article
- A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage.Microbiome · 2018Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationThe Sequence Read Archive (SRA) contains raw data from many different types of sequence projects. As of 2017, the SRA contained approximately ten petabases of DNA sequence (10 16 bp). Annotations of the data are provided by the submitter, and mining the data in the SRA is complicated by both the amount of data and the detail within those annotations. Here, we introduce PARTIE, a partition engine optimized to differentiate sequence read data into metagenomic (random) and amplicon (targeted) sequence data sets.
resultsPARTIE subsamples reads from the sequencing file and calculates four different statistics: k -mer frequency, 16S abundance, prokaryotic- and viral-read abundance. These metrics are used to create a RandomForest decision tree to classify the sequencing data, and PARTIE provides mechanisms for both supervised and unsupervised classification. We demonstrate the accuracy of PARTIE for classifying SRA data, discuss the probable error rates in the SRA annotations and introduce a resource assessing SRA data. AVAILABILITY AND IMPLEMENTATION: PARTIE and reclassified metagenome SRA entries are available from https://github.com/linsalrob/partie. CONTACT: redwards@mail.sdsu.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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