Spaced seeds improve k-mer-based metagenomic classification

February 22, 2015 · Entered Twilight · 🏛 Bioinform.

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Repo contents: .gitmodules, README.rst, scripts, section.3.1.2, section.3.2, section.3.3, section.3.4, seed-kraken

Authors Karel Brinda, Maciej Sykulski, Gregory Kucherov arXiv ID 1502.06256 Category q-bio.GN Cross-listed cs.CE, cs.LG Citations 93 Venue Bioinform. Repository https://github.com/gregorykucherov/spaced-seeds-for-metagenomics ⭐ 13 Last Checked 1 month ago

Abstract

Metagenomics is a powerful approach to study genetic content of environmental samples that has been strongly promoted by NGS technologies. To cope with massive data involved in modern metagenomic projects, recent tools [4, 39] rely on the analysis of k-mers shared between the read to be classified and sampled reference genomes. Within this general framework, we show in this work that spaced seeds provide a significant improvement of classification accuracy as opposed to traditional contiguous k-mers. We support this thesis through a series a different computational experiments, including simulations of large-scale metagenomic projects. Scripts and programs used in this study, as well as supplementary material, are available from http://github.com/gregorykucherov/spaced-seeds-for-metagenomics.