diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 6aef7521ab1..e9772b19593 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -281,6 +281,10 @@
-->
+
diff --git a/tools/solid_tools/solid_qual_boxplot.xml b/tools/solid_tools/solid_qual_boxplot.xml
new file mode 100644
index 00000000000..b72e4890241
--- /dev/null
+++ b/tools/solid_tools/solid_qual_boxplot.xml
@@ -0,0 +1,36 @@
+
+ for SOLiD data
+
+ qualsolid_boxplot_graph.sh -t '$input.name' -i $input -o $output
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Creates a boxplot graph for the quality scores in the library.
+
+.. class:: infomark
+
+**TIP:** Use the **Quality Statistics for SOLiD data** tool to generate the report file needed for this tool.
+
+-----
+
+**Output Example**
+
+* Black horizontal lines are medians
+* Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
+* Whiskers show outlier at max. 1.5*IQR
+
+
+.. image:: ../static/images/solid_qual.png
+
+
+
+
diff --git a/tools/solid_tools/solid_qual_stats.py b/tools/solid_tools/solid_qual_stats.py
new file mode 100644
index 00000000000..8ec8e932f74
--- /dev/null
+++ b/tools/solid_tools/solid_qual_stats.py
@@ -0,0 +1,140 @@
+#! /usr/bin/python
+#Guruprasad Ananda
+
+import sys, os, zipfile, tempfile
+
+QUAL_UPPER_BOUND = 41
+QUAL_LOWER_BOUND = 1
+
+def stop_err( msg ):
+ sys.stderr.write( "%s\n" % msg )
+ sys.exit()
+
+def unzip( filename ):
+ zip_file = zipfile.ZipFile( filename, 'r' )
+ tmpfilename = tempfile.NamedTemporaryFile().name
+ for name in zip_file.namelist():
+ file( tmpfilename, 'a' ).write( zip_file.read( name ) )
+ zip_file.close()
+ return tmpfilename
+
+def __main__():
+
+ infile_score_name = sys.argv[1].strip()
+ fout = open(sys.argv[2].strip(),'r+w')
+
+ infile_is_zipped = False
+ if zipfile.is_zipfile( infile_score_name ):
+ infile_is_zipped = True
+ infile_name = unzip( infile_score_name )
+ else:
+ infile_name = infile_score_name
+
+ readlen = None
+ j = 0
+ for line in file( infile_name ):
+ line = line.strip()
+ if not(line) or line.startswith("#") or line.startswith(">"):
+ continue
+ elems = line.split()
+ try:
+ for item in elems:
+ assert int(item)
+ if not(readlen):
+ readlen = len(elems)
+ if len(elems) != readlen:
+ print "Note: Reads in the input dataset are of variable lengths."
+ j += 1
+ except:
+ invalid_lines += 1
+ if j > 10:
+ break
+
+ invalid_lines = 0
+ position_dict = {}
+ print >>fout, "column\tcount\tmin\tmax\tsum\tmean\tQ1\tmed\tQ3\tIQR\tlW\trW"
+ for k,line in enumerate(file( infile_name )):
+ line = line.strip()
+ if not(line) or line.startswith("#") or line.startswith(">"):
+ continue
+ elems = line.split()
+ if position_dict == {}:
+ for pos in range(readlen):
+ position_dict[pos] = [0]*QUAL_UPPER_BOUND
+ if len(elems) != readlen:
+ invalid_lines += 1
+ continue
+ for ind,item in enumerate(elems):
+ try:
+ item = int(item)
+ position_dict[ind][item]+=1
+ except:
+ pass
+
+ invalid_positions = 0
+ for pos in position_dict:
+ carr = position_dict[pos] #count array for position pos
+ total = sum(carr) #number of bases found in this column.
+ med_elem = int(round(total/2.0))
+ lowest = None #Lowest quality score value found in this column.
+ highest = None #Highest quality score value found in this column.
+ median = None #Median quality score value found in this column.
+ qsum = 0.0 #Sum of quality score values for this column.
+ q1 = None #1st quartile quality score.
+ q3 = None #3rd quartile quality score.
+ q1_elem = int(round((total+1)/4.0))
+ q3_elem = int(round((total+1)*3/4.0))
+
+ try:
+ for ind,cnt in enumerate(carr):
+ qsum += ind*cnt
+
+ if cnt!=0:
+ highest = ind
+
+ if lowest==None and cnt!=0: #first non-zero count
+ lowest = ind
+
+ if q1==None:
+ if sum(carr[:ind+1]) >= q1_elem:
+ q1 = ind
+
+ if median==None:
+ if sum(carr[:ind+1]) < med_elem:
+ continue
+ median = ind
+ if total%2 == 0: #even number of elements
+ median2 = median
+ if sum(carr[:ind+1]) < med_elem+1:
+ for ind2,elem in enumerate(carr[ind+1:]):
+ if elem != 0:
+ median2 = ind+ind2+1
+ break
+ median = (median + median2)/2.0
+
+
+ if q3==None:
+ if sum(carr[:ind+1]) >= q3_elem:
+ q3 = ind
+
+
+ mean = qsum/total #Mean quality score value for this column.
+ iqr = q3-q1
+ left_whisker = max(q1 - 1.5*iqr,lowest)
+ right_whisker = min(q3 + 1.5*iqr,highest)
+
+ print >>fout,"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" %(pos+1,total,lowest,highest,qsum,mean,q1,median,q3,iqr,left_whisker,right_whisker)
+ except:
+ invalid_positions += 1
+ nullvals = ['NA']*11
+ print >>fout,"%s\t%s" %(pos+1,'\t'.join(nullvals))
+
+ if invalid_lines:
+ print "Skipped %d reads as invalid." %invalid_lines
+ if invalid_positions:
+ print "Skipped stats computation for %d read postions." %invalid_positions
+
+if __name__=="__main__":
+ __main__()
+
+
diff --git a/tools/solid_tools/solid_qual_stats.xml b/tools/solid_tools/solid_qual_stats.xml
new file mode 100644
index 00000000000..50d952055a1
--- /dev/null
+++ b/tools/solid_tools/solid_qual_stats.xml
@@ -0,0 +1,65 @@
+
+ for SOLiD data
+ solid_qual_stats.py $input $output1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Creates quality statistics report for the given SOLiD quality score file.
+
+.. class:: infomark
+
+**TIP:** This statistics report can be used as input for **Quality Boxplot for SOLiD data** tool.
+
+-----
+
+**The output file will contain the following fields:**
+
+* column = column number (position on the read)
+* count = number of bases found in this column.
+* min = Lowest quality score value found in this column.
+* max = Highest quality score value found in this column.
+* sum = Sum of quality score values for this column.
+* mean = Mean quality score value for this column.
+* Q1 = 1st quartile quality score.
+* med = Median quality score.
+* Q3 = 3rd quartile quality score.
+* IQR = Inter-Quartile range (Q3-Q1).
+* lW = 'Left-Whisker' value (for boxplotting).
+* rW = 'Right-Whisker' value (for boxplotting).
+
+
+
+
+
+**Output Example**::
+
+ column count min max sum mean Q1 med Q3 IQR lW rW
+ 1 6362991 2 32 250734117 20.41 5 9 28 23 2 31
+ 2 6362991 2 32 250531036 21.37 10 26 30 20 5 31
+ 3 6362991 2 34 248722469 19.09 10 26 30 20 5 31
+ 4 6362991 2 34 247654797 18.92 10 26 30 20 5 31
+ .
+ .
+ 32 6362991 2 31 143436943 16.54 3 10 25 22 2 31
+ 33 6362991 2 32 114269843 16.96 3 10 25 22 2 31
+ 34 6362991 2 29 140638447 12.10 3 10 25 22 2 29
+ 35 6362991 2 29 138910532 11.83 3 10 25 22 2 29
+
+
+
+