A pipeline is a general sofware tool to incorporate different aligners or variant calling algorithms.Using pipelines, a biologist can perform efficient NGS data analysis.NGS data analysis involves several steps which need to be suitably designed and arranged into an efficient procedure as it involves huge data, which can be done using pipelines. The software interface in a Pipeline tool provides an easy and user-friendly environment for various NGS data analysis procedures like annotation,variant calling, visualization, duplicate marking etc. Various pipeline algorithms and software tools are available to achieve each step in the workflow of NGS data analysis. An example pipeline for Second Generation Sequencing is given below:
