skip to main content
Language:
Search Limited to: Search Limited to: Resource type Show Results with: Show Results with: Search type Index

Bracken: estimating species abundance in metagenomics data

PeerJ. Computer science, 2017-01, Vol.3, p.e104, Article e104 [Peer Reviewed Journal]

COPYRIGHT 2017 PeerJ. Ltd. ;2017 Lu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Computer Science) and either DOI or URL of the article must be cited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;ISSN: 2376-5992 ;EISSN: 2376-5992 ;DOI: 10.7717/peerj-cs.104

Full text available

Citations Cited by
  • Title:
    Bracken: estimating species abundance in metagenomics data
  • Author: Lu, Jennifer ; Breitwieser, Florian P ; Thielen, Peter ; Salzberg, Steven L
  • Subjects: Abundance ; Analysis ; Bacteria ; Bayesian analysis ; Bayesian estimation ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Estimation ; Gene sequencing ; Genomes ; Medical research ; Metagenomics ; Methods ; Microbial populations ; Microbiome ; Microorganisms ; Ribonucleic acid ; Ribosomal RNA ; RNA ; Species abundance ; Taxonomy ; Tuberculosis
  • Is Part Of: PeerJ. Computer science, 2017-01, Vol.3, p.e104, Article e104
  • Description: 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.
  • Publisher: San Diego: PeerJ. Ltd
  • Language: English
  • Identifier: ISSN: 2376-5992
    EISSN: 2376-5992
    DOI: 10.7717/peerj-cs.104
  • Source: Open Access: PubMed Central
    AUTh Library subscriptions: ProQuest Central
    DOAJ Directory of Open Access Journals
Back to results list
INSPIRE LIBRARY - TON DUC THANG UNIVERSITY (84-028) 37 755 057 Feedback
19 Nguyen Huu Tho St. Dist.7, HCM thuvien@tdtu.edu.vn

Copyright © 2017 INSPIRE LIBRARY - TON DUC THANG UNIVERSITY

Searching Remote Databases, Please Wait