Poster Open Access

ProPhyle: a phylogeny-based metagenomic classifier using the Burrows-Wheeler Transform

Břinda, Karel; Salikhov, Kamil; Pignotti, Simone; Kucherov, Gregory

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  "DOI": "10.5281/zenodo.1045427", 
  "abstract": "<p>Metagenomics is a powerful approach to study genetic content of environmental samples and it has been strongly promoted by Next-Generation Sequencing technologies. The aim of metagenomic classification is to assign each sequence of the metagenome to a corresponding taxonomic unit, or to classify it as \u201cnovel\u201d.</p>\n\n<p>To cope with increasingly large metagenomic projects, researchers resort to alignment-free methods. The most popular tool \u2013 Kraken \u2013 provides an extremely rapid read classification, but its index suffers from two major limitations: an enormous memory consumption and a lossy <em>k</em>-mer representation through their lowest common ancestors.</p>\n\n<p>We present Prophyle, a metagenomic classifier based on the Burrows-Wheeler Transform. ProPhyle uses a classification algorithm similar to Kraken but with an indexing strategy based on a bottom-up propagation of <em>k</em>-mers in the tree, assembling contigs at each node and matching using a standard full-text search. The obtained index occupies only a fraction of RAM compared to Kraken \u2013 13 GB instead of 90 GB for index construction and 14 GB instead of 72\u00a0GB for index querying. The resulting index is also more expressive, allowing users to retrieve a list of <em>all</em> genomes for every queried <em>k</em>-mer. Overall, ProPhyle provides an index for resource-frugal metagenomic classification, which is accurate even with single-species phylogenetic trees. Prophyle is available at, released under the MIT license.</p>", 
  "author": [
      "family": "B\u0159inda, Karel"
      "family": "Salikhov, Kamil"
      "family": "Pignotti, Simone"
      "family": "Kucherov, Gregory"
  "id": "1045427", 
  "issued": {
    "date-parts": [
  "language": "eng", 
  "publisher": "Zenodo", 
  "title": "ProPhyle: a phylogeny-based metagenomic classifier using the Burrows-Wheeler Transform", 
  "type": "graphic"
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