title: Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data.
abstract: BACKGROUND
  Identification of biological specimens is a requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but generally do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances.
  
  
  RESULTS
  We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on genome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100% identification accuracy at supra-species level and 78% accuracy at the species level.
  
  
  CONCLUSIONS
  CNIDARIA allows for fast, resource-efficient comparison and identification of both raw and assembled genome and transcriptome data. This can help answer both fundamental (e.g. in phylogeny, ecological diversity analysis) and practical questions (e.g. sequencing quality control, primer design).
authors.affiliation: Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands. sauloalves.aflitos@wur.nl.|Bioinformatics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands. sauloalves.aflitos@wur.nl.
authors.forename: Saulo Alves
authors.initials: SA
authors.lastname: Aflitos
authors.affiliation: Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands. severing@mpipz.mpg.de.
authors.forename: Edouard
authors.initials: E
authors.lastname: Severing
authors.affiliation: Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands. gabino.sanchezperez@wur.nl.|Bioinformatics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands. gabino.sanchezperez@wur.nl.
authors.forename: Gabino
authors.initials: G
authors.lastname: Sanchez-Perez
authors.affiliation: Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands. sander.peters@wur.nl.
authors.forename: Sander
authors.initials: S
authors.lastname: Peters
authors.affiliation: Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands. hans.deJong@wur.nl.
authors.forename: Hans
authors.initials: H
authors.lastname: de Jong
authors.affiliation: Bioinformatics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands. dick.deridder@wur.nl.
authors.forename: Dick
authors.initials: D
authors.lastname: de Ridder
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D016678:Genome; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D007313:Insecta / Q000145:classification / Q000235:genetics; D020407:Internet; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D019657:Solanaceae / Q000145:classification / Q000235:genetics; D059467:Transcriptome; D014584:User-Computer Interface