MetaPalette: a <italic toggle="yes">k</italic>-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation

ABSTRACT Metagenomic profiling is challenging in part because of the highly uneven sampling of the tree of life by genome sequencing projects and the limitations imposed by performing phylogenetic inference at fixed taxonomic ranks. We present the algorithm MetaPalette, which uses long k-mer sizes (...

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Autores principales:	David Koslicki, Daniel Falush
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	taxonomic profiling metagenomics quantitative methods Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/e78a8718c7fa438ca1aa8c5cc8c2b0a0
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spelling	oai:doaj.org-article:e78a8718c7fa438ca1aa8c5cc8c2b0a02021-12-02T18:39:34ZMetaPalette: a <italic toggle="yes">k</italic>-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation10.1128/mSystems.00020-162379-5077https://doaj.org/article/e78a8718c7fa438ca1aa8c5cc8c2b0a02016-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00020-16https://doaj.org/toc/2379-5077ABSTRACT Metagenomic profiling is challenging in part because of the highly uneven sampling of the tree of life by genome sequencing projects and the limitations imposed by performing phylogenetic inference at fixed taxonomic ranks. We present the algorithm MetaPalette, which uses long k-mer sizes (k = 30, 50) to fit a k-mer “palette” of a given sample to the k-mer palette of reference organisms. By modeling the k-mer palettes of unknown organisms, the method also gives an indication of the presence, abundance, and evolutionary relatedness of novel organisms present in the sample. The method returns a traditional, fixed-rank taxonomic profile which is shown on independently simulated data to be one of the most accurate to date. Tree figures are also returned that quantify the relatedness of novel organisms to reference sequences, and the accuracy of such figures is demonstrated on simulated spike-ins and a metagenomic soil sample. The software implementing MetaPalette is available at: https://github.com/dkoslicki/MetaPalette . Pretrained databases are included for Archaea, Bacteria, Eukaryota, and viruses. IMPORTANCE Taxonomic profiling is a challenging first step when analyzing a metagenomic sample. This work presents a method that facilitates fine-scale characterization of the presence, abundance, and evolutionary relatedness of organisms present in a given sample but absent from the training database. We calculate a “k-mer palette” which summarizes the information from all reads, not just those in conserved genes or containing taxon-specific markers. The compositions of palettes are easy to model, allowing rapid inference of community composition. In addition to providing strain-level information where applicable, our approach provides taxonomic profiles that are more accurate than those of competing methods. Author Video: An author video summary of this article is available.David KoslickiDaniel FalushAmerican Society for Microbiologyarticletaxonomic profilingmetagenomicsquantitative methodsMicrobiologyQR1-502ENmSystems, Vol 1, Iss 3 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	taxonomic profiling metagenomics quantitative methods Microbiology QR1-502
spellingShingle	taxonomic profiling metagenomics quantitative methods Microbiology QR1-502 David Koslicki Daniel Falush MetaPalette: a <italic toggle="yes">k</italic>-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
description	ABSTRACT Metagenomic profiling is challenging in part because of the highly uneven sampling of the tree of life by genome sequencing projects and the limitations imposed by performing phylogenetic inference at fixed taxonomic ranks. We present the algorithm MetaPalette, which uses long k-mer sizes (k = 30, 50) to fit a k-mer “palette” of a given sample to the k-mer palette of reference organisms. By modeling the k-mer palettes of unknown organisms, the method also gives an indication of the presence, abundance, and evolutionary relatedness of novel organisms present in the sample. The method returns a traditional, fixed-rank taxonomic profile which is shown on independently simulated data to be one of the most accurate to date. Tree figures are also returned that quantify the relatedness of novel organisms to reference sequences, and the accuracy of such figures is demonstrated on simulated spike-ins and a metagenomic soil sample. The software implementing MetaPalette is available at: https://github.com/dkoslicki/MetaPalette . Pretrained databases are included for Archaea, Bacteria, Eukaryota, and viruses. IMPORTANCE Taxonomic profiling is a challenging first step when analyzing a metagenomic sample. This work presents a method that facilitates fine-scale characterization of the presence, abundance, and evolutionary relatedness of organisms present in a given sample but absent from the training database. We calculate a “k-mer palette” which summarizes the information from all reads, not just those in conserved genes or containing taxon-specific markers. The compositions of palettes are easy to model, allowing rapid inference of community composition. In addition to providing strain-level information where applicable, our approach provides taxonomic profiles that are more accurate than those of competing methods. Author Video: An author video summary of this article is available.
format	article
author	David Koslicki Daniel Falush
author_facet	David Koslicki Daniel Falush
author_sort	David Koslicki
title	MetaPalette: a <italic toggle="yes">k</italic>-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
title_short	MetaPalette: a <italic toggle="yes">k</italic>-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
title_full	MetaPalette: a <italic toggle="yes">k</italic>-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
title_fullStr	MetaPalette: a <italic toggle="yes">k</italic>-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
title_full_unstemmed	MetaPalette: a <italic toggle="yes">k</italic>-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
title_sort	metapalette: a <italic toggle="yes">k</italic>-mer painting approach for metagenomic taxonomic profiling and quantification of novel strain variation
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/e78a8718c7fa438ca1aa8c5cc8c2b0a0
work_keys_str_mv	AT davidkoslicki metapaletteaitalictoggleyeskitalicmerpaintingapproachformetagenomictaxonomicprofilingandquantificationofnovelstrainvariation AT danielfalush metapaletteaitalictoggleyeskitalicmerpaintingapproachformetagenomictaxonomicprofilingandquantificationofnovelstrainvariation
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MetaPalette: a <italic toggle="yes">k</italic>-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation

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