Pipeline for amplicon sequencing projects. OTUs can be build with various methods (usearch,vsearch,uparse,swarm) and classified using the RDP Classifier and SINA. Final output is a BIOM file for downstream processing (Phyloseq/R)
License: MIT License
Hi,
I am trying to run through your pipeline and I managed to get to the point where taxonomic assignment is done.
The rule lca is using a taxref file /data/db/pr2/gb203/lotus_lca.tax but I am a bit puzzled as to how this file was created.
Do you have a script for that, or could you tell how the format of that file is defined?
Thanks in advance!
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