title: ParTIES: a toolbox for Paramecium interspersed DNA elimination studies.
abstract: BACKGROUND
  Developmental DNA elimination occurs in a wide variety of multicellular organisms, but ciliates are the only single-celled eukaryotes in which this phenomenon has been reported. Despite considerable interest in ciliates as models for DNA elimination, no standard methods for identification and characterization of the eliminated sequences are currently available.
  
  
  RESULTS
  We present the Paramecium Toolbox for Interspersed DNA Elimination Studies (ParTIES), designed for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms.
  
  
  METHODS
  ParTIES is multi-threaded Perl software available at https://github.com/oarnaiz/ParTIES. ParTIES is distributed under the GNU General Public Licence v3.
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
authors.forename: Cyril
authors.initials: C
authors.lastname: Denby Wilkes
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Arnaiz
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
authors.forename: Linda
authors.initials: L
authors.lastname: Sperling
mesh_terms: D016770:Ciliophora Infections / Q000235:genetics*; D016054:DNA, Protozoan / Q000378:metabolism*; D018503:Genome, Protozoan; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D010247:Paramecium / Q000235:genetics* / Q000302:isolation & purification; D015800:Protozoan Proteins / Q000378:metabolism*; D012984:Software
chemical_list: D016054:DNA, Protozoan; D015800:Protozoan Proteins