{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T11:31:28Z","timestamp":1763551888728},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2017,6,15]],"date-time":"2017-06-15T00:00:00Z","timestamp":1497484800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Genome sequencing projects sometimes uncover more organisms than expected, especially for complex and\/or non-model organisms. It is therefore useful to develop software to identify mix of organisms from genome sequence assemblies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here we present PhylOligo, a new package including tools to explore, identify and extract organism-specific sequences in a genome assembly using the analysis of their DNA compositional characteristics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The tools are written in Python3 and R under the GPLv3 Licence and can be found at https:\/\/github.com\/itsmeludo\/Phyloligo\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx396","type":"journal-article","created":{"date-parts":[[2017,6,13]],"date-time":"2017-06-13T11:09:47Z","timestamp":1497352187000},"page":"3283-3285","source":"Crossref","is-referenced-by-count":24,"title":["PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies"],"prefix":"10.1093","volume":"33","author":[{"given":"Ludovic","family":"Mallet","sequence":"first","affiliation":[{"name":"INRA UR875, Unit\u00e9 Math\u00e9matiques et Informatique Appliqu\u00e9es de Toulouse (MIAT), Auzeville, Castanet-Tolosan, France"}]},{"given":"Tristan","family":"Bitard-Feildel","sequence":"additional","affiliation":[{"name":"CNRS UMR7590, Sorbonne Universit\u00e9s, Universit\u00e9 Pierre et Marie Curie \u2013 Paris 6, MNHN, IRD \u2013 IUC, Paris, France"}]},{"given":"Franck","family":"Cerutti","sequence":"additional","affiliation":[{"name":"INRA UR875, Unit\u00e9 Math\u00e9matiques et Informatique Appliqu\u00e9es de Toulouse (MIAT), Auzeville, Castanet-Tolosan, France"}]},{"given":"H\u00e9l\u00e8ne","family":"Chiapello","sequence":"additional","affiliation":[{"name":"INRA UR875, Unit\u00e9 Math\u00e9matiques et Informatique Appliqu\u00e9es de Toulouse (MIAT), Auzeville, Castanet-Tolosan, France"}]}],"member":"286","published-online":{"date-parts":[[2017,6,15]]},"reference":[{"key":"2023020207520986700_btx396-B1","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1038\/nmeth.3103","article-title":"Binning metagenomic contigs by coverage and composition","volume":"11","author":"Alneberg","year":"2014","journal-title":"Nat. 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