Ruby script to execute all commands in the QIIME overview tutorial, but including denoising and chimera check.
Works with QIIME 1.7
Usage: qiime_pipe.rb [options]
-h, --help Display this screen
-s, --file_sff <file> SFF file to process
-m, --file_map <file> Mapping file to process
-o, --dir_out <dir> Output directory
-f, --force Force overwrite log file and output directory
-d, --denoise Denoise data
-c, --chimera Chimera filter data
-D, --chimera_db <file> Chimere database (/home/maasha/Install/QIIME1.6/data/Gold/gold.fa)
-b, --barcode_size <int> Size of barcodes used (10)
-C, --cpus <int> Number of CPUs to use (1)
-e, --email <string> Send email alert