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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

• Frequently Asked Questions
  • How to deal with ambiguous nucleotides?
  • When is an appropriate time to check for chimeras?
  • How to use the output of the --internal-structure option to produce network representations?
  • Does swarm require sequences to all be of the same length?
  • Can swarm work on short/long sequences?
  • Swarm's scalability
• Preparing your sample
• Working with several samples (dereplication, contingency tables)
• Working with third-party pipelines (Mothur, QIIME, Uparse)
• Working with very large datasets
• Subtleties of pairwise alignments
• Swarm as a compression method
• Advantages of swarm over prefix clustering
• Get fasta sequences for all amplicons in a given OTU