Name: bpipe-qiime_closed_otus
Owner: Melbourne Bioinformatics
Description: bpipe-qiime_pick_closed_otus
Created: 2014-05-09 01:09:27.0
Updated: 2014-07-16 16:09:52.0
Pushed: 2014-05-12 04:08:55.0
Homepage: null
Size: 156
Language: Groovy
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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