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RepeatExplorer

RepeatExplorer

RepeatExplorer pipeline tool is for the identification and characterization of DNA repeats in plant and animal genomes using high-throughput data sets. The RepeatExplorer algorithm utilizes graph-based clustering.

Topic

DNA polymorphism; Mobile genetic elements

Details

  • Operation: Repeat sequence detection; Genome annotation
  • Input: FASTQ; FASTA
  • Output: FASTA; HTML
  • Software interface: Command-line user interface; Galaxy server
  • Language: R;Perl;Python
  • Operating system: Linux
  • License: GNU GPL v3
  • Cost: Free
  • Version name: 2.3.7, 0.3.7
  • Maturity: Mature
  • Credit: The Ministry of Education, Youth and Sports of the Czech Republic, the Academy of Sciences of the Czech Republic
  • Contact: petr _at_ umbr.cas.cz | petr _at_ umbr.cas.cz
  • Collection: -

Publications

Novák P, Neumann P, Macas J "Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data." BMC Bioinformatics 2010 https://doi.org/10.1186/1471-2105-11-378
PMID: 20633259
PMCID: PMC2912890


Novák P, Neumann P, Pech J, Steinhaisl J, Macas J "RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads." Bioinformatics, 2013 https://doi.org/10.1093/bioinformatics/btt054
PMID: 23376349
PMCID: None


Download and documentation




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