Identification and genetic characterization of a novel Orthobunyavirus species by a straightforward high-throughput sequencing-based approach

Shifman, Ohad; Cohen-Gihon, Inbar; Beth-Din, Adi; Zvi, Anat; Laskar, Orly; Paran, Nir; Epstein, Eyal; Stein, Dana; Dorozko, Marina; Wolf, Dana; Yitzhaki, Shmuel; Shapira, Shmuel C.; Melamed, Sharon; Israeli, Ofir

Bioinformatic analyses. Sequencing reads were trimmed by 3 bases at the 5′ ends, and reads originating from the Vero cells were filtered out using SAMtools 40 against the Chlorocebus sabaeus genome. The reads were subjected to taxonomical profiling with MetaPhlAn2 41 using the default settings. Subsequent taxonomical profiling was performed with Pathoscope 2.0 42 using an in-house-constructed target genome database containing all complete bacterial, viral and fungal genomes from the National Center for Biotechnology Information (NCBI) database (5414, 5777 and 3451 genomes, respectively). The reads were aligned to these genome sequences using the Bowtie2 algorithm 43 with default Pathoscope parameters. De novo assembly of the reads was performed by SPAdes, with default parameters 44 , and Velvet 45 , using VelvetOptimiser 46 to determine the optimized parameters for the assembly.