Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Aflitos, Saulo; Severing, Edouard; Sanchez-Perez, Gabino; Peters, Sander; de Jong, Hans; de Ridder, Dick
• Is Part Of: BMC bioinformatics. Volume 16:Issue 1(2015)
• Page Start: 1
• Page End: 10
• Publication Date: 2015-12
• Subjects: Clustering -- k-mer -- NGS -- RNA-seq -- Phylogeny -- Species identification; Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-015-0806-7
• Languages: English
• ISSNs: 1471-2105

Abstract

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. Conclusion 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).