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
  4. incorporate the Q values
  5. output contigs
  6. output SNPs

Usage: perl RGA_blat_SNP_Q_rc3.pl options
 required:
  -r    reference sequence(s) in a single FASTA file
  -s    source (seq) in a single FASTA file
  -q    Q scores (prb) in a single FASTA file
 optional:
  -e    error_rate [optional, by default: 0.00]
  -b    BLAT results file [optional]
  -o    10.ooc file (ABSOLUTE path, e.g., /home/bpp/shenr/bin/10.occ. Note: 10.ooc file could accelerate BLAT by up to 40 times)
                !!! UPDATE: 10.ooc file is not approprіate for Solexa reads - this option is DISABLED!
  -t    BLAT stepSize [optional, by default: 1;  if -b is provided, this will be ignored]
  -l    BLAT tileSize [optional, by default: 10; if -b is provided, this will be ignored]
  -v    Q value cutoff [optional, by default: 20 in -40:40]
  -n    total SNP cutoff [optional, by default: 3]
  -m    replace any position with 'N' in contig if the total number of reads is <= the value specified
  -p    candidate SNP percent cutoff [optional, by default: 0.70 <70%>]