RGA - Reference Guided Assember. It does:
  1. calcuate the real coverage of Solexa microreads to the reference sequence(s)
  2. report the coordinates of all the maximum contigs and length
  3. output density graphes of chromosome size

Usage: perl RGA_blat_rc1.pl options
 required:
  -r    reference sequence(s) in a single FASTA file
  -i    input file (sequences) in a single FASTA file
 optional:
  -e    error_rate [optional, by default: 0.00]; calculate: (# of mismatches) / (read length)
  -b    BLAT results file [optional]
  -t    BLAT tileSize [optional, range in [6, 15], by default: 10; if -b is provided, this will be ignored]
  -s    BLAT stepSize [optional, range in [1, tileSize], by default: 1; if -b is provided, this will be ignored]
  -p    switch of plotting or not [by default: not plot] (need gnuplot v4.2.2 or later in search path)