期刊论文详细信息
BMC Bioinformatics
Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data
Software
Sander Peters1  Saulo Alves Aflitos2  Gabino Sanchez-Perez2  Dick de Ridder3  Hans de Jong4  Edouard Severing4 
[1] Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands;Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands;Bioinformatics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands;Bioinformatics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands;Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands;
关键词: Clustering;    k-mer;    NGS;    RNA-seq;    Phylogeny;    Species identification;   
DOI  :  10.1186/s12859-015-0806-7
 received in 2015-07-11, accepted in 2015-10-29,  发布年份 2015
来源: Springer
PDF
【 摘 要 】

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).

【 授权许可】

CC BY   
© Aflitos et al. 2015

【 预 览 】
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