Abstract
BackgroundIdentification 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.ResultsWe 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.ConclusionCNIDARIA 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).Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0806-7) contains supplementary material, which is available to authorized users.
Highlights
Identification of biological specimens is a requirement for a range of applications
Data set To validate the performance of CNIDARIA, we gathered a collection of 135 genomic, transcriptomic and raw Next Generation Sequencing (NGS) datasets covering a wide range of organisms
We have introduced CNIDARIA, a tool to quickly and reliably analyse Whole Genome Sequencing (WGS) and RNA sequencing (RNA-seq) samples from both assembled and unassembled NGS data, offering significant advantages in terms of time and space requirements compared to a state-of-the-art tool
Summary
Identification of biological specimens is a requirement for a range of applications. Unequivocal identification of biological specimens is a major requirement for reliable and reproducible (bio)medical research, control of intellectual property by biological patent holders, regulating the flow of biological specimen across national borders, enforcing the Nagoya protocol [1] and verifying the authenticity of claims of the biological source of products by customs authority. Probe-based technologies include microarrays, PCR probes, DNA fingerprinting and immunoassays involving the hybridization of DNA samples with predetermined sets of probes or primers. Such methods are cheap and allow precise identification, but may fail in cases where.
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