Journal: Genome Medicine
Article Title: Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
Figure Lengend Snippet: Metagenomic sequencing workflow for MinION nanopore sequencing compared to Illumina MiSeq sequencing. a Overall workflow. b Steps in the MetaPORE real-time analysis pipeline. The turnaround time for sample-to-detection nanopore sequencing, defined here as the cumulative time taken for nucleic acid extraction, reverse transcription, library preparation, sequencing, MetaPORE bioinformatics analysis, and pathogen detection, was under 6 hr, while Illumina sequencing took over 20 hr. The time differential is accounted for by increased times for library quantitation, sequencing, and bioinformatics analysis with the Illumina protocol. *Assumes a 12-hr 50-bp single-end MiSeq run of ~12–15 million reads, with 50 bp the minimum estimated read length needed for accurate pathogen identification. **Denotes estimated average SURPI bioinformatics analysis run length for MiSeq data [ 19 ]. The stopwatch is depicted as a 12-hr clock
Article Snippet: Example 1: Nanopore sequencing of high-titer chikungunya virus (Flow cell #1) To test the ability of nanopore sequencing to identify metagenomic reads from a clinical sample, we first analyzed a plasma sample harboring high-titer CHIKV and previously sequenced on an Illumina MiSeq platform (Fig. ) [ ].
Techniques: Sequencing, Nanopore Sequencing, Quantitation Assay