OPTIONS

--i, input file (required)
--o, output file (required)    
--lib, library type  (default is sanger)    
--dup, remove duplicate reads
--qf, filter by phred probability (quality)
--dist, std deviations between Phred min and mean
--lf, filter by read length
--truseq, removes truseq adapters from reads
--trim_l, trim reads starting at left end
--trim_r, trim reads starting at left end
--adpt, remove a user supplied adapter      
--fasta, convert to fastA format 
--dna_rna, convert reads to RNA
--rev_comp, reverse complement reads
--no_n, remove non-designated bases from reads
--help, Print this help