Fig. 1: Schematic of the mNGS assay workflow. | Nature Communications

Fig. 1: Schematic of the mNGS assay workflow.

From: Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery

Fig. 1

A RNA from respiratory samples is extracted and treated with DNase. Internal control is added to assess human background during sequencing. Human rRNA is depleted during cDNA synthesis. Libraries are generated on the automated Tecan MagicPrep NGS instrument. Libraries are normalized, pooled, and loaded onto the sequencer. B Sequences are processed using SURPI+ software for alignment and classification. Reads are preprocessed by trimming of adapters and removal of low-quality/low-complexity sequences, followed by computational subtraction of human reads. Reads are mapped to the closest matched genome to identify non-overlapping regions using NCBI GenBank and FDA-ARGOS database. To aid in analysis, automated result summaries, heat maps of both raw and normalized read counts, and coverage and pairwise identity plots are generated for clinical interpretation. Total turnaround time is between 14 and 22 h depending on type of sequencer used.

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