ArticlePeerJ. Computer science2017
Bracken: estimating species abundance in metagenomics data.
Article in PeerJ. Computer science, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,354 papers.
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1,354 citing papers in PubMed.
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- Not all stress is equal: Examination stress and cortisol reactivity are associated with exploratory species-level variation but not broad restructuring of the gut microbiome.Neurobiology of stress · 2026Article
- Sex- and Time-Resolved Physiological and Gut Ecosystem Responses to a Food-Grade Microbiome-Targeted Intervention in Collegiate Endurance Athletes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Effects of a low dose of 3-nitrooxypropanol and a combination of direct-fed microbials on methane emission, oral swab bacterial community, and performance in dairy cows.Journal of animal science and biotechnology · 2026Article
- The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome.eLife · 2026Article
- Expansion of pathogens and restoration of human skin microbiome in CD4 T-cell lymphopenia.The Journal of investigative dermatology · 2026Article
- Gut microbiome shifts in chronic systolic heart failure are associated with disease severity and clinical improvement.Nature cardiovascular research · 2026Article
- Subclinical Mastitis and Antibiotic Exposure Reshape the Milk Bacteriome, Resistome, and Metabolic Functional Profiles in Dairy Cows.MicrobiologyOpen · 2026Article
- Piezophilic activity dominates the Puerto Rico Trench deep subseafloor biosphere.bioRxiv : the preprint server for biology · 2026Article
- Photoperiod driven modulation of behavior, gut microbiota, and brain transcriptomics in zebrafish.Pflugers Archiv : European journal of physiology · 2026Article
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- Multi-kingdom gut microbiota analyses identify biomarkers of different types of pediatric short bowel syndrome.mSystems · 2026Article
- Insights into the dynamics of antibiotic resistance genes in the human gut microbiome across populations.Gut pathogens · 2026Article
- Comparative Transcriptomic Analysis Reveals Conserved and Nutrient-Specific Responses to Nutrient Deficiencies in Quinoa.Plants (Basel, Switzerland) · 2026Article
1,294 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.
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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 OpenQuestion graph.