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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<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:creator>Břinda, Karel</dc:creator>
  <dc:creator>Salikhov, Kamil</dc:creator>
  <dc:creator>Pignotti, Simone</dc:creator>
  <dc:creator>Kucherov, Gregory</dc:creator>
  <dc:date>2017-07-24</dc:date>
  <dc:description>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”.

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 k-mer representation through their lowest common ancestors.

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 k-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 all genomes for every queried k-mer. Overall, ProPhyle provides an index for resource-frugal metagenomic classification, which is accurate even with single-species phylogenetic trees. Prophyle is available at http://github.com/karel-brinda/prophyle, released under the MIT license.</dc:description>
  <dc:identifier>https://zenodo.org/record/1045427</dc:identifier>
  <dc:identifier>10.5281/zenodo.1045427</dc:identifier>
  <dc:identifier>oai:zenodo.org:1045427</dc:identifier>
  <dc:language>eng</dc:language>
  <dc:relation>doi:10.5281/zenodo.1045426</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/</dc:rights>
  <dc:title>ProPhyle: a phylogeny-based metagenomic classifier using the Burrows-Wheeler Transform</dc:title>
  <dc:type>info:eu-repo/semantics/conferencePoster</dc:type>
  <dc:type>poster</dc:type>
</oai_dc:dc>

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