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Welcome to the swarm wiki!

I designed swarm as a clustering method, and a clustering method only, not a full-metabarcoding pipeline like qiime or mothur. The spirit is to do one thing, but to do it right.

The down-side is that it can be difficult to use swarm results if you are not comfortable building your own pipeline. This is why I present Fred's metabarcoding pipeline, describing how to go from fastq files to OTU tables with vsearch, cutadapt and swarm.

Please feel free to comment, create issues or email me.