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