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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  <identifier identifierType="DOI">10.5281/zenodo.1045427</identifier>
      <creatorName>Břinda, Karel</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0003-0200-557X</nameIdentifier>
      <affiliation>CCDD Harvard TH Chan School of Public Health</affiliation>
      <creatorName>Salikhov, Kamil</creatorName>
      <affiliation>LIGM Université Paris-Est</affiliation>
      <creatorName>Pignotti, Simone</creatorName>
      <affiliation>LIGM Université Paris-Est</affiliation>
      <creatorName>Kucherov, Gregory</creatorName>
      <affiliation>LIGM/CNRS Université Paris-Est</affiliation>
    <title>Prophyle: A Phylogeny-Based Metagenomic Classifier Using The Burrows-Wheeler Transform</title>
    <date dateType="Issued">2017-07-24</date>
  <resourceType resourceTypeGeneral="Text">Poster</resourceType>
    <alternateIdentifier alternateIdentifierType="url"></alternateIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1045426</relatedIdentifier>
    <rights rightsURI="">Creative Commons Attribution 4.0</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
    <description descriptionType="Abstract">&lt;p&gt;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 “novel”.&lt;/p&gt;

&lt;p&gt;To cope with increasingly large metagenomic projects, researchers resort to alignment-free methods. The most popular tool – Kraken – provides an extremely rapid read classification, but its index suffers from two major limitations: an enormous memory consumption and a lossy &lt;em&gt;k&lt;/em&gt;-mer representation through their lowest common ancestors.&lt;/p&gt;

&lt;p&gt;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 &lt;em&gt;k&lt;/em&gt;-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 – 13 GB instead of 90 GB for index construction and 14 GB instead of 72 GB for index querying. The resulting index is also more expressive, allowing users to retrieve a list of &lt;em&gt;all&lt;/em&gt; genomes for every queried &lt;em&gt;k&lt;/em&gt;-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.&lt;/p&gt;</description>
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