title: SRIdent: A novel pipeline for real-time identification of species from high-throughput sequencing reads in Metagenomics and clinical diagnostic assays.
abstract: New advances in rapid sequencing of large amounts of DNA have brought a great potential for the study of complex communities of microorganisms. One of the challenging problems is rapid identification of species from sequenced reads. Delays in the identification of pathogens are a barrier to the early diagnosis and proper treatment of infectious diseases. In this paper we proposed SRIdent (Short Read Identifier), an effective pipeline for real-time identification of species from high-throughput sequencing reads in Metagenomics and clinical diagnostic assays. This pipeline is based on generating k-mers from the short reads and searching the existence of DNA signatures in the Reads k-mers, by using Apache Hive data-warehousing. RkmerG (Read k-mers Generator) is a software program presented in this paper, for producing k-mers of the short reads, in order to use in the pipeline. The purpose of this study is to identify the species in a sample, directly from the reads without assembling and alignment.
authors.forename: Ramin
authors.initials: R
authors.lastname: Karimi
authors.forename: Andras
authors.initials: A
authors.lastname: Hajdu
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000032:analysis*; D030541:Databases, Genetic; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D056186:Metagenomics; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D013045:Species Specificity
chemical_list: D004247:DNA