Pipeline for 3rd Generation sequencing data from MinION The Vir-MinION pipeline works on 3rd generation data and provide the user with a taxonomic classification of the reads through three strategies: assem-bly-based, read-based, and clustering-based. The pipelines supply the scientist with comprehen-sive results in graphical and textual format for future analyses. Finally, the pipelines equip the us-er with a stand-alone platform with dedicated and various viral databases, a requirement for working in field conditions without internet connection.

Vir-MinION requires few arguments to run, and its syntax is intuitive

Usage: VirMinION-Pipe.sh PreProcDataFolder PreProcOutFolder BaseCallConfFile BarCodeKit NumOfThread Method [--read_based | --ass_based | --clust_based]

Refer to Vir-MinION_Installation_Manual.pdf to install and configure Vir-MinION on your NVIDIA machine

Refer to Vir-MinION_User_Manual.pdf for a quick use of Vir-MinION

Refer to VIRMINION-CAMISIM_DEEPSIM.txt for generating synthetic data using CAMISIM/DEEPSIM and run Vir-MinION using it. If you prefer to use synthetic data used during the Vir-MinION test, download the following file multi_viruses_fast5.tgz (https://github.com/emiliomastriani/Vir-MinION/blob/main/multi_viruses_fast5.tgz)

Refer to CreateDBs.txt for a step-by-step guide on installing and configuring the DBs need by Vir-MinION