title: Implementation of a Non-Human Primate Model of Ebola Disease: Infection of Mauritian    Cynomolgus Macaques and Analysis of Virus Populations
design: The viral RNA were amplified specifically in eigh fragments by RT-PCR using the SuperScript® III One-Step RT-PCR System with Platinum® Taq High Fidelity kit (Thermo Fisher Scientific) and specific primers. ). PCR products were pooled in equimolar proportions for library building. After a physical fragmentation (sonication) in 200bp fragments, libraries were built using the automated AB Library Builder System (ThermoFisher Scientific). To pool equimolarly the barcoded samples a quantification step by the 2100 Bioanalyzer instrument (Agilent Technologies) was realized. An emulsion PCR of the pools was prepared using the automated Ion OneTouch 2 platform (ThermoFisher Scientific). The barcoded-pooled sample was loaded on a 316v2 chip and the sequencing reaction was performed on the PGM device (ThermoFisher Scientific)  following manufacturer’s instructions. Automated read datasets provided by Torrent software suite 5.0.2 were trimmed according to quality score (99%) and length (reads shorter than 30bp were removed) using CLC genomics workbench software (CLC bio-Qiagen). Primers used for RT-PCR were removed using an in-house software package. Reads were mapped on reference (inoculum strain) using CLC. A de novo contig was also produced to ensure that the consensus sequence was not affected by the reference sequence.