Package - attempt to pick otus, summarize taxa, summarize otu run alpha and beta diversity on both unrarefacted data and rarefacted data
./commands.sh [options] application [arguments]
-h, --help show brief help
-i, --INPUT=input_file specify an input file to run
-o, --DIR=output_dir specify a output directory
-l, --LOG=log_file specify a log file to report
-p, --PY=path_of_ninja.py specify the path of ninja.py
-t, --TREE=reference_tree specify the tree of otu reference
-s, --SIM=similarity specify the minimum percent similarity
-d, --DB=base directory of code specify the environment
Make sure the dataset directory(i.e. the directory that contains the input fna file) has the same name with the dataset itself. Also, the -d for the base directory should be the directory that contains the bin and data directories.
The script would run all the analysis with non-rarefaction at first and gives an suggested rarefaction depth, then the user inputs a expected depth to continue the script with all the analysis with rarefaction.