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Fig. 2 | Genome Medicine

Fig. 2

From: Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

Fig. 2

Metagenomic identification of CHIKV and EBOV from clinical blood samples by nanopore sequencing. a Time line of sequencing runs on flow cell #1 with sample reloading, plotted as a function of elapsed time in hours since the start of flow cell sequencing. b Cumulative numbers of all sequenced reads (black line) and target viral reads (red line) from the Chik1 run (left panel) and Ebola1 run (right panel), plotted as a function of individual sequencing run time in minutes. c Taxonomic donut charts generated using the MetaPORE bioinformatics analysis pipeline from the Chik1 run (left panel) and Ebola1 run (right panel). The total number of reads analyzed is shown in the center of the donut. d Coverage plots generated in MetaPORE by mapping reads aligning to CHIKV (left, Chik1 run) or EBOV (right, Ebola1 run) to the closest matching reference genome ((e), asterisk). A corresponding pairwise identity plot is also shown for CHIKV, for which there is sufficient coverage. e Whole-genome phylogeny of CHIKV. Representative CHIKV genome sequences from the Asian-Pacific clade, including the Puerto Rico PR-S6 strain recovered by nanopore and MiSeq sequencing, or all available 188 near-complete or complete CHIKV genomes (inset), are included. Branch lengths are drawn proportionally to the number of nucleotide substitutions per position, and support values are shown for each node. were was analyzed in MetaPORE on a 64-core Ubuntu Linux server using the June 2014 and January 2015 NT databases as the reference databases for the CHIKV and EBOV samples, respectively

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