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A new method for decontamination of de novo transcriptomes using a hierarchical clustering algorithm.
Lafond-Lapalme, Joël; Duceppe, Marc-Olivier; Wang, Shengrui; Moffett, Peter; Mimee, Benjamin.
Afiliação
  • Lafond-Lapalme J; Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada.
  • Duceppe MO; Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
  • Wang S; Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada.
  • Moffett P; Département d'informatique, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
  • Mimee B; Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
Bioinformatics ; 33(9): 1293-1300, 2017 05 01.
Article em En | MEDLINE | ID: mdl-28011783
ABSTRACT
Motivation 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.

Results:

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. Availability and Implementation Scripts and documentation about the MCSC decontamination method are available at https//github.com/Lafond-LapalmeJ/MCSC_Decontamination . Contact benjamin.mimee@agr.gc.ca. Supplementary information Supplementary data are available at Bioinformatics online.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Software / Análise de Sequência de RNA / Transcriptoma Tipo de estudo: Prognostic_studies Limite: Animals Idioma: En Ano de publicação: 2017 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Software / Análise de Sequência de RNA / Transcriptoma Tipo de estudo: Prognostic_studies Limite: Animals Idioma: En Ano de publicação: 2017 Tipo de documento: Article