Pseudoalignment for metagenomic read assignment

Schaeffer, Lorian; Pimentel, Harold; Bray, Nicolas; Melsted, Páll; Pachter, Lior

doi:10.48550/arxiv.1510.07371

Cited by 1 publication

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“…Our approach thus uses all k-mers of a particular length in the reference dataset, while discarding the specific information provided by matches of individual k-mers. This is similar in spirit to the so-called pseudoalignment approach of [44] except here we use k-mer counts of the entire sample, not of individual reads whose origins may be ambiguous. We model these palettes using a simple linear mixture model which includes both the reference organisms and "hypothetical organisms" at different degrees of genetic relatedness to the reference organisms.…”

Section: Introductionmentioning

confidence: 99%

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

Koslicki

Falush

2016

mSystems

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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.

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Section: Introductionmentioning

confidence: 99%