ArticleBioinformatics (Oxford, England)2011
Mixture models for analysis of the taxonomic composition of metagenomes.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
- Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling.Microbiome · 2018Article
- Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities.BMC bioinformatics · 2017Article
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- Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses.Briefings in bioinformatics · 2015Article
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- ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.PloS one · 2015Article
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- Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries.Microbiome · 2015Article
- AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization.BMC bioinformatics · 2014Article
- Exploring neighborhoods in the metagenome universe.International journal of molecular sciences · 2014Article
- MosaicSolver: a tool for determining recombinants of viral genomes from pileup data.Nucleic acids research · 2014Article
- Article
- FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares.PeerJ · 2014Article
- Article
- Article
- Fragment assignment in the cloud with eXpress-D.BMC bioinformatics · 2013Article
- Protein signature-based estimation of metagenomic abundances including all domains of life and viruses.Bioinformatics (Oxford, England) · 2013Article
- MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.Genome biology · 2013Article
- Streaming fragment assignment for real-time analysis of sequencing experiments.Nature methods · 2013Article
- Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective.Briefings in bioinformatics · 2012Review
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3 authors.
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Abstract
motivationInferring the taxonomic profile of a microbial community from a large collection of anonymous DNA sequencing reads is a challenging task in metagenomics. Because existing methods for taxonomic profiling of metagenomes are all based on the assignment of fragmentary sequences to phylogenetic categories, the accuracy of results largely depends on fragment length. This dependence complicates comparative analysis of data originating from different sequencing platforms or resulting from different preprocessing pipelines.
resultsWe here introduce a new method for taxonomic profiling based on mixture modeling of the overall oligonucleotide distribution of a sample. Our results indicate that the mixture-based profiles compare well with taxonomic profiles obtained with other methods. However, in contrast to the existing methods, our approach shows a nearly constant profiling accuracy across all kinds of read lengths and it operates at an unrivaled speed. AVAILABILITY: A platform-independent implementation of the mixture modeling approach is available in terms of a MATLAB/Octave toolbox at http://gobics.de/peter/taxy. In addition, a prototypical implementation within an easy-to-use interactive tool for Windows can be downloaded.
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