Welcome to the CAMP!

The MetaSUB Core Modular Analysis Pipeline, the CAMP, is a software toolkit designed for dynamic and educational analyses of metagenomes, bacterial isolates, and, in general, all things microbial. It is the primary analytic workflow for the MetaSUB consortium.

The core philosophy of the CAMP is anchored in modularity, which is meant to stand in stark contrast to the popular bioinformatic toolkits of “one-click pipelines.” By defining every step in an analytic workflow as single, consistently documented and parameterized codebase, we aim to enable users to gain total control over and a deep understand of their bioinformatic analyses. For more information on our design philosophy, check out the Introduction section.

Notifications about CAMP releases will be available through the MetaSUB Twitter account.

Please post questions and issues related to CAMP tools on the GitHub repository of the specific module in question.

Note

The CAMP is under active development.

Citing the CAMP

If you use the CAMP, please site it (as well as the software it wraps!) as described in references.

Getting started

• Introduction
• Installation and deployment

The CAMP modules

• Short-Read Quality Control
• Short-Read Taxonomy
• Short-Read Assembly
• Gene Catalog
• Binning
• Nanopore Quality Control
• MAG Quality Control

Developing for the CAMP

• Developing for the CAMP
• Upcoming modules