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001-es BibID:	bibEBI00026092
Első szerző:	Karimi, Ramin (programtervező matematikus)
Cím:	SRIdent : a novel pipeline for real-time identification of species from high-throughput sequencing reads in metagenomics and clinical diagnostic assays / Ramin Karimi, András Hajdu
Dátum:	2015
Megjegyzések:	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 datawarehousing. 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.
Tárgyszavak:	Természettudományok Matematika- és számítástudományok tanulmány, értekezés DNA Sequential analysis Pipelines Microorganisms Genomics Bioinformatics Databases
Megjelenés:	37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Milan, 2015. Proceedings. - p. 6481-6484
További szerzők:	Hajdu András (1973-) (matematikus, informatikus)
Pályázati támogatás:	OTKA-101680 OTKA SROP-4.2.2.B-15/1/KONV-2015-0001 Egyéb
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