Extended Data Fig. 6: Length distributions of pathogen cfDNA in mNGS data.
From: Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids
Analysis is performed on the 87 body fluid samples sequenced on both Illumina and nanopore platforms. a, Diagram showing how original genomic DNA lengths are recovered. Paired-end sequencing data is aligned to either a human or microbial genome, followed by determination of fragment length from the start and end positions and construction of a read length histogram. b, Histogram of average DNA lengths for human, bacterial, and fungal organisms obtained from mNGS data. Human DNA is observed to peak at the stereotypical 160 bp nucleosome footprint; both bacterial and fungal DNA are most abundant at sizes of <100 bp, but a higher molecular weight tail is observed extending to 500–600 bp. c, Histogram of bacterial read lengths according to sequencing platform. Illumina and nanopore sequencing platforms produce different size distributions. d, Length analysis of mNGS reads for samples with 16S PCR performed. Comparison of the length profiles of the 16S discordant bacteria cases (S31 and S88), 16S concordant bacteria cases (mean of S10, S36, S41, S69, S85, S128), and all bacteria mean. The pathogen cfDNA in cases S31 and S88 are more fragmented, with the vast majority of fragments <300 bp. The relative paucity of longer fragments could hinder 16S PCR amplification.
