Antarctic lakes provide excellent study sites for investigating microbial ecology. Specifically, the lakes are diverse in physical and chemical characteristics yet located in the same region. Additionally, the systems have simple community structures which enables analysis to derive a more complete picture. I developed a metagenomics analysis pipeline to process incoming samples from a recent winter-over expedition. The pipeline was designed submit various workflows to the local HPC in an automated fashion reducing errors, user input, and increasing the longevity of data products. The entire project consists of over 3000 lines of custom script.