Virome pipeline is a general pipeline constructed for viral metagenomes analysis from NGS read data. The pipeline integrates a series of open source tools, including STAR, MegaHit, BBmap, BLAST, ORFfinder and CAP3, which listed above are required when running the pipeline. In addition, Perl and R language environment are need to install and configure on the machine before running the pipeline.

./Pipeline/virome_pipeline.sh /data/input /data/output sample_name sample_host /data/database /package

./data/input: path to input directory

./data/output: path to output directory

./sample_name: Used for directory name of sample

./sample_host: host type of sample, value = "Culicoides" or "Mosquito"

./data/database: Path to reference files and database files directory

./package: Path to bioinformatics tools directory

Liu Lin, Shen Qin, Li Nan, He Yuwen, Pan Mei, Jin Yuting, Meng Jinxin, Wang Jinglin, Wu Aiping; Comparative viromes reveals the diversity, consistency and specificity of viral compositions in culicoides and mosquitos