Fig 1. Flowchart of NGS-QCbox pipeline illustrating the two modes of usage namely quick and complete.

NGS-QCbox comprises of two workflow modes namely quick and complete. In quick mode, read/base level metrics are computed in parallel using Raspberry, an in-house tool, both before and after quality trimming. On the other hand, complete mode is full-fledged quality control and variant calling pipeline that integrates quick mode and additionally generates genome coverage information in parallel. Quality of the data generated could be assessed using this information.