Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. There are several existing batch adjustment tools for -omics data, but they do not indicate a priori whether adjustment needs to be conducted or how correction should be applied. We present a software pipeline, BatchQC, which addresses these issues using interactive visualizations and statistics that evaluate the impact of batch effects in a genomic dataset. BatchQC can also apply existing adjustment tools and allow users to evaluate their benefits interactively. We used the BatchQC pipeline on both simulated and real data to demonstrate the effectiveness of this software toolkit.