Bioinformatic analyses are often performed in a stepwise manner, with the output of 1 analysis being used as the input for the next. These multistep, multisoftware analyses are frequently referred to as pipelines and are often set up to run automatically from 1 step to the next without input from the user. Different puoblic pipelines for WGS analysis are available but many use in-house developed pipelines, customized depending on organism and purpose.