Patho-finder-A fast and accurate program for pathogen identification through RNA-seq
Journal
Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Pages
1148-1151
Date Issued
2015
Author(s)
Abstract
Technology of next generation sequencing to detect pathogens of sample can impact human health by revealing pathogens which cause disease. Several workflow has developed in purposed to detect pathogens in next generation sequencing data. However, the requirement of computation power of these workflows limited the application. The time consuming problem make the workflow difficult to detect datasets with large sample size. Here we presented Patho-finder, a fast and accurate workflow designed for detecting pathogen in RNA sequencing data. We have evaluated performance of Patho-finder by three aspects. First, we evaluate performance by alter the data features, to see how Patho-finder work under different simulation conditions. Next, we compare the time consuming and accuracy between Patho-finder and existing workflow. At last, we used Patho-finder on the RNA-seq of cell lines with known virus-infected. The validation result demonstrated our approach could finish the task in real datasets. ? 2015 IEEE.
Subjects
next generation sequencing; pathogen; RNA-seq
SDGs
Other Subjects
Bioinformatics; Cell culture; RNA; Viruses; Computation power; Human health; Next-generation sequencing; Pathogen identification; Real data sets; Rna sequencing; Sample sizes; Validation results; Pathogens
Type
conference paper