IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoringKatrina L Kalantar, Tiago Carvalho, Charles F A de Bourcy, Boris Dimitrov, Greg Dingle, Rebecca Egger, Julie Han, Olivia B Holmes, Yun-Fang Juan, Ryan King, Andrey Kislyuk, Michael F Lin, Maria Mariano, Todd Morse, Lucia V Reynoso, David Rissato Cruz, Jonathan Sheu, Jennifer Tang, James Wang, Mark A Zhang, Emily Zhong, Vida Ahyong, Sreyngim Lay, Sophana Chea, Jennifer A Bohl, Jessica E Manning, Cristina M Tato, Joseph L DeRisi
Oxford Academic, 2020Abstract: Metagenomic next-generation sequencing (mNGS) has enabled the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Existing mNGS data analysis tools typically require bioinformatics expertise and access to local server-class hardware resources. For many research laboratories, this presents an obstacle, especially in resource-limited environments.
