NAME

SYNOPSIS

--i, input file (required)
--lib, library type         
--path, path to input fiile (required)
--smry, return summary statistics 
--dup, remove duplicate reads
--qf, filter by read quality
--lf, filter by read length
--trim_l, trim reads starting at left end
--trim_r, trim reads starting at left end
--adpt_l, remove a left end adapter 
--mis_l, permit mismatches between left end adapter and read      
--adpt_r, remove a right end adapter
--mis_r, permit mismatches between left end adapter and read
--fasta, convert to fastA format 
--rna, convert reads to RNA
--rev_comp, reverse complement reads
--no_n, remove non-designated bases from reads
--clean, remove temp files 
--help, Print this help