AmQUB Pipeline

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 │ ┌── [A m Q U B]  
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This pipeline is an attempt to better automate the Borneman Lab's targeted amplicon microbiome analysis pipeline, which uses Qiime2, Usearch, and Blast for taxonomic assignments. (AmpliconQiime2UsearchBlast)

Many of the python, perl, and R helper functions that these scripts call were written by Paul Ruegger.

Currently, the pipeline requires a 64-bit license to Usearch. (32-bit is available for free, but it won't run large datasets.) All other required software is freely available.

Vsearch integration is planned as well.