mNGS of Homo sapiens nasopharynx
Library preparation was performed per the manufacturer's instructions. An initial equivolume library pool was generated, and the quality and quantity assessed by electrophoresis (High-Sensivity DNA Kit and Agilent Bioanalyzer; Agilent Technologies, Santa Clara, CA, USA) and small-scale sequencing on an Illumina iSeq machine (Illumina, San Diego, CA, USA). Subsequent equimolar pooling of individual librairies proceeded to large-scale paired end mNGS (2 x 146 bp) on an Illumina NextSeq platform (Illumina, San Diego, CA, USA). The pipeline used to separate sequencing output of individual librairies into fastq files of paired end reads is at : https://github.com/czbiohub/utilities.