Fig. 3

MetaPORE analysis of Illumina MiSeq data from samples containing CHIKV and EBOV. Taxonomic donut charts were generated from Illumina MiSeq data corresponding to the Chik1 run (a) and Ebola1 run (b) using the MetaPORE bioinformatics analysis pipeline. The total number of MiSeq reads analyzed is shown in the center of the donut. Note that given computational time constraints, only a subset of reads (n = 100,000) was analyzed using MetaPORE. Coverage and pairwise identity plots were generated from MiSeq CHIKV reads from the Chik1 sample (248,677 of 3,235,099 reads, 7.7 %) (c), or EBOV reads from the Ebola1 sample (20,820 of 2,743,589 reads, 0.76 %)  (d), identified using SURPI analysis and LASTZ mapping {Harris, 2007 #34} at an e-value of 10-5 to the closest matching reference genome. Data were 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.