title: A new method for decontamination of de novo transcriptomes using a hierarchical clustering algorithm.
abstract: The identification of contaminating sequences in a de novo assembly is challenging because of the absence of information on the target species. For sample types where the target organism is impossible to isolate from its matrix, such as endoparasites, endosymbionts and soil-harvested samples, contamination is unavoidable. A few post-assembly decontamination methods are currently available but are based only on alignments to databases, which can lead to poor decontamination.
  
  
  
  We present a new decontamination method based on a hierarchical clustering algorithm called MCSC. This method uses frequent patterns found in sequences to create clusters. These clusters are then linked to the target species or tagged as contaminants using classic alignment tools. The main advantage of this decontamination method is that it allows sequences to be tagged correctly even if they are unknown or misaligned to a database.
  
  
  
  Scripts and documentation about the MCSC decontamination method are available at https://github.com/Lafond-LapalmeJ/MCSC_Decontamination .
  
  
  
  : benjamin.mimee@agr.gc.ca.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada.|Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
authors.forename: Joël
authors.initials: J
authors.lastname: Lafond-Lapalme
authors.affiliation: Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada.
authors.forename: Marc-Olivier
authors.initials: MO
authors.lastname: Duceppe
authors.affiliation: Département d'informatique, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
authors.forename: Shengrui
authors.initials: S
authors.lastname: Wang
authors.affiliation: Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
authors.forename: Peter
authors.initials: P
authors.lastname: Moffett
authors.affiliation: Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Mimee
mesh_terms: D000465:Algorithms; D000818:Animals; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome; D017187:Tylenchida / Q000235:genetics; D048889:Weevils / Q000235:genetics / Q000469:parasitology