bpipe-qiime_pick_closed_otus
A pipeline to assign otu's for 16S reads from fastq files.
Uses nesoni clip for primer removal (custom ion torrent primers and linkers)
Uses a custom perl script to produce a valid qiime file mapping text file
Uses 16S database as specified at the top of the qiime_pipeline.groovy file.
Requires a variant of the bpipe script to handle module specification. If this is not used, then the required modules must be loaded in the relevant .bashrc script...
bpipe variant: slugger70-bpipe