TaxAss is a Taxonomy Assignment workflow that lets you classify 16S datasets using two different taxonomy reference databases. TaxAss was developed so that the McMahon Lab's Freshwater Training Set (the FreshTrain) could be used for taxonomy assignment alongside comprehensive databases like Greengenes or Silva. We believe TaxAss will also work with other custom databases (so if that's you, get in touch!)
Step-by-step directions: tax-scripts/TaxAss_Directions.html
TaxAss uses a series of python, R, and bash scripts in addition to using BLAST+ and mothur's classify.seqs() command. The scripts are sourced from the terminal window (mac or linux). You'll need to download this repository (green "Clone or download" button, top right), and then just add the tax-scripts folder to your working diriectory.
The stuff you need:
- Step by step directions are in
TaxAss_Directions.html
inside thetax-scripts
folder (view without download here). - Scripts are in the
tax-scripts
folder. - The FreshTrain taxonomy files are in the
FreshTrain-files
folder.
The stuff you can ignore:
- Scripts to process & edit the FreshTrain arb files are in the
arb-scripts
folder - Scripts for making poster/paper figures are in
figure-scripts
folder. - A pdf of my ISME16 poster (that might be a good overview):
poster-ISME16.pdf
Please tell me! If you find a bug (or if you get confused) I want to fix it/help you. If you're all github savvy you can submit an issue, or you can just send me an e-mail with TaxAss in the title: robin.rohwer@gmail.com
The McMahon lab studies lake microbial ecology (and some of it also studies wastewater). We are at the Univerisity of Wisconsin-Madison.
Lab Website: https://mcmahonlab.wisc.edu/
Lab Twitter: @mcmahonlab