code: def spades(args):
      
      from jcvi.formats.fastq import readlen
  
      p = OptionParser(spades.__doc__)
      opts, args = p.parse_args(args)
  
      if len(args) == 0:
          sys.exit(not p.print_help())
  
      folder, = args
      for p, pf in iter_project(folder):
          rl = readlen([p[0], "--silent"])
  
          # <http://spades.bioinf.spbau.ru/release3.1.0/manual.html#sec3.4>
          kmers = None
          if rl >= 150:
              kmers = "21,33,55,77"
          elif rl >= 250:
              kmers = "21,33,55,77,99,127"
  
          cmd = "spades.py"
          if kmers:
              cmd += " -k {0}".format(kmers)
          cmd += " --careful"
          cmd += " --pe1-1 {0} --pe1-2 {1}".format(*p)
          cmd += " -o {0}_spades".format(pf)
          print(cmd)
docs: %prog spades folder
  
      Run automated SPADES.