NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline.

ABSTRACT: Metagenomic sequencing combined with Oxford Nanopore Technology has the potential to become a point-of-care test for infectious disease in public health and clinical settings, providing rapid diagnosis of infection, guiding individual patient management and treatment strategies, and informing infection prevention and control practices. However, publicly available, streamlined, and reproducible pipelines for analyzing Nanopore metagenomic sequencing data are still lacking. Here we introduce NanoSPC, a scalable, portable and cloud compatible pipeline for analyzing Nanopore sequencing data. NanoSPC can identify potentially pathogenic viruses and bacteria simultaneously to provide comprehensive characterization of individual samples. The pipeline can also detect single nucleotide variants and

SUBMITTER: Xu Y 

PROVIDER: S-EPMC7319573 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature