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Welcome to the SWARM wiki!

The objective of these pages is to provide our users with more documentation than provided in Swarm's manual. That wiki provides space to describe a typical workflow, to give ready-to-use command line examples, and to deal with specific cases such as compatibility with existing pipelines.

Table of contents

• Preparing your sample
• [Working with several samples](https://github.com/torognes/swarm/wiki/Working with several samples) (dereplication, contingency tables)
• [Working with third-party pipelines](https://github.com/torognes/swarm/wiki/Working with third-party pipelines) (Mothur, QIIME, Uparse)