  Motivation: Accurate data analysis and quality control is critical for
metagenomic studies. Though many tools exist to analyze metagenomic data there
is no consistent framework to integrate and run these tools across projects.
Currently, computational analysis of metagenomes is time consuming, often
misses potentially interesting results, and is difficult to reproduce. Further,
comparison between metagenomic studies is hampered by inconsistencies in tools
and databases.
  Results: We present the MetaSUB Core Analysis Pipeline (CAP) a comprehensive
tool to analyze metagenomes and summarize the results of a project. The CAP is
designed in a bottom up fashion to perform QC, preprocessing, analysis and even
to build relevant databases and install necessary tools.
  Availability and Implementation: The CAP is available under an MIT License on
GitHub at https://github.com/MetaSUB/CAP2 and on the Python Package Index.
Documentation and examples are available on GitHub.
