README
Version 9/12/2016
This python wrapper picks reference based OTUs using NINJA-OPS and the Green Genes database, then generates standard QIIME outputs with and without rarefaction applied. Note that without rarefaction applied, the OTU table will be normalized prior to Bray-Curtis metric calculation only.
PREREQUISITES:
1. Version 1.5.1 of NINJA-OPS must be installed and added to the PATH environment variable
2. The green genes database must be installed and path to appropriate tree must be provided as an argument
3. Dependencies: QIIME 1.9.1, Python 2.7, BIOM 2.1+
usage: do.qiime.py [-h] -i INPUTFILE -o OUTPUTDIR -t GGTREEFILE [-s {0}]
-h, --help show this help message and exit
REQUIRED:
-i INPUTFILE, --inputfile INPUTFILE
Raw sequences file
-o OUTPUTDIR, --outputdir OUTPUTDIR
Output directory
-t GGTREEFILE, --ggtreefile GGTREEFILE
Green Genes tree file
OPTIONAL:
-r {rarefaction,norarefaction,both}, --rarefaction {rarefaction,norarefaction,both}
Run with rarefaction only, without rarefaction, or with both.
-l RAREFACTIONLEVEL, --rarefactionlevel RAREFACTIONLEVEL
Rarefaction level, if known {positive integer} (required if running with rarefaction only)
-b OTUTABLE, --otutable OTUTABLE
OTU table in BIOM format for generating rarefied QIIME output only
-s {0}, --similarity {0}
Similarity threshold for OTU clustering {number between 0 and 1}, default: .97
EXAMPLES:
1. [Default behavior] Picks OTUs on raw sequences, then generates QIIME output without rarefaction, then prompts the user to pick a rarefaction depth before proceeding with generated rarefied QIIME output.
do.qiime.py -i seqs.fna -o ./output -t ./trees/97_otus.tree
2. Pick OTUs on raw sequences, then generate QIIME output without rarefaction. This is useful for large datasets that are to be run in the background and does not wait for user input.
do.qiime.py -i seqs.fna -o ./output -t ./trees/97_otus.tree -r norarefaction
3. Pick OTUs on raw sequences, then generate QIIME output with rarefaction only, subsampling at a depth of 1000 sequences per sample. This is useful for large datasets that are to be run in the background. You should determine the rarefaction level prior to running this (e.g. examine the non-rarefied OTU table BIOM summary output).
do.qiime.py -i seqs.fna -o ./output -t ./trees/97_otus.tree -r rarefaction -b ./otutable.biom -l 1000
4. Picks OTUs on raw sequences, then generates QIIME output without rarefaction, then generates rarefied QIIME output with a predetermined rarefaction level of 1000 sequences per depth (not recommended unless you are sure about your desired depth).
do.qiime.py -i seqs.fna -o ./output -t ./trees/97_otus.tree -l 1000