Poster Open Access

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

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

MARC21 XML Export

<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="">
  <datafield tag="041" ind1=" " ind2=" ">
    <subfield code="a">eng</subfield>
  <controlfield tag="005">20171222231142.0</controlfield>
  <controlfield tag="001">1045427</controlfield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">LIGM Université Paris-Est</subfield>
    <subfield code="a">Salikhov, Kamil</subfield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">LIGM Université Paris-Est</subfield>
    <subfield code="a">Pignotti, Simone</subfield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">LIGM/CNRS Université Paris-Est</subfield>
    <subfield code="a">Kucherov, Gregory</subfield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">632711</subfield>
    <subfield code="z">md5:28ffd9a73b6a88248248f4443284eccb</subfield>
    <subfield code="u"></subfield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  <datafield tag="260" ind1=" " ind2=" ">
    <subfield code="c">2017-07-24</subfield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="p">openaire</subfield>
    <subfield code="p">user-bioinformatics</subfield>
    <subfield code="o"></subfield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="u">CCDD Harvard TH Chan School of Public Health</subfield>
    <subfield code="0">(orcid)0000-0003-0200-557X</subfield>
    <subfield code="a">Břinda, Karel</subfield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">ProPhyle: a phylogeny-based metagenomic classifier using the Burrows-Wheeler Transform</subfield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-bioinformatics</subfield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="u"></subfield>
    <subfield code="a">Creative Commons Attribution 4.0 International</subfield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2"></subfield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&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;</subfield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="n">doi</subfield>
    <subfield code="i">isVersionOf</subfield>
    <subfield code="a">10.5281/zenodo.1045426</subfield>
  <datafield tag="024" ind1=" " ind2=" ">
    <subfield code="a">10.5281/zenodo.1045427</subfield>
    <subfield code="2">doi</subfield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">poster</subfield>
All versions This version
Views 149149
Downloads 8383
Data volume 52.5 MB52.5 MB
Unique views 147147
Unique downloads 7979


Cite as