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MetaPalette - mSystems

835 views · Published 2 August 2016 · 3:00 · Indexed 28 October 2026

Channel: ASM - Microbes Make Our World · 2016 · Science & Technology

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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.

MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation

David Koslicki, Daniel Falush

Janet K. Jansson, Editor

Published in mSystems on 07 June 2016
Direct link: http://msystems.asm.org/content/1/3/e00020-16

mSystems™ publishes preeminent work that stems from applying technologies for high-throughput analyses to achieve insights into the metabolic and regulatory systems at the scale of both the single cell and microbial communities. The scope of mSystems™ encompasses all important biological and biochemical findings drawn from analyses of large data sets, as well as new computational approaches for deriving these insights. mSystems™ welcomes submissions from researchers who focus on the microbiome, genomics, metagenomics, transcriptomics, metabolomics, proteomics, glycomics, bioinformatics, and computational microbiology. mSystems™ provides streamlined decisions, while carrying on ASM's tradition of rigorous peer review.
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