diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 645cb00c2ee..b00a14540b9 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -19,7 +19,7 @@
     </datatype>
     <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true">
       <converter file="fastqsolexa_to_fasta_converter.xml" target_datatype="fasta"/>
-      <converter file="fastqsolexa_to_qual_converter.xml" target_datatype="qual"/>
+      <converter file="fastqsolexa_to_qual_converter.xml" target_datatype="qualsolexa"/>
     </datatype>
     <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"/>
     <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true">
@@ -42,7 +42,9 @@
     </datatype>
     <datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
     <datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
-    <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" display_in_upload="true"/>
+    <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
+    <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/>
+    <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
     <datatype extension="scf" type="galaxy.datatypes.images:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
     <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
@@ -186,7 +188,9 @@
     <sniffer type="galaxy.datatypes.sequence:Maf"/>
     <sniffer type="galaxy.datatypes.sequence:Lav"/>
     <sniffer type="galaxy.datatypes.sequence:csFasta"/>
-    <sniffer type="galaxy.datatypes.qualityscore:QualityScore"/>
+    <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSolexa"/>
+    <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
+    <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
     <sniffer type="galaxy.datatypes.sequence:Fasta"/>
     <sniffer type="galaxy.datatypes.sequence:FastqSolexa"/>
     <sniffer type="galaxy.datatypes.interval:Wiggle"/>
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
index fcf966626b7..c8c8c48147a 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
@@ -4,7 +4,7 @@
     <param format="fastqsolexa" name="input1" type="data" label="Choose Fastqsolexa file"/>
   </inputs>
   <outputs>
-    <data format="qual" name="output1" />
+    <data format="qualsolexa" name="output1" />
   </outputs>
   <help>
   </help>
diff --git a/lib/galaxy/datatypes/qualityscore.py b/lib/galaxy/datatypes/qualityscore.py
index 8367cbf979f..275f58529df 100644
--- a/lib/galaxy/datatypes/qualityscore.py
+++ b/lib/galaxy/datatypes/qualityscore.py
@@ -9,11 +9,11 @@ from galaxy import util
 
 log = logging.getLogger(__name__)
 
-class QualityScore ( data.Text ):
+class QualityScoreSOLiD ( data.Text ):
     """
     until we know more about quality score formats
     """
-    file_ext = "qual"
+    file_ext = "qualsolid"
     
     def set_peek( self, dataset, line_count=None ):
         if not dataset.dataset.purged:
@@ -21,7 +21,7 @@ class QualityScore ( data.Text ):
             if line_count is None:
                 dataset.blurb = data.nice_size( dataset.get_size() )
             else:
-                dataset.blurb = "%s lines, Quality score file" % util.commaify( str( line_count ) )
+                dataset.blurb = "%s lines, SOLiD Quality score file" % util.commaify( str( line_count ) )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -30,15 +30,80 @@ class QualityScore ( data.Text ):
         try:
             return dataset.peek
         except:
-            return "Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) )
+            return "SOLiD Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) )
 
     def sniff( self, filename ):
         """
         >>> fname = get_test_fname( 'sequence.fasta' )
-        >>> QualityScore().sniff( fname )
+        >>> QualityScoreSOLiD().sniff( fname )
         False
-        >>> fname = get_test_fname( 'sequence.qual' )
-        >>> QualityScore().sniff( fname )
+        >>> fname = get_test_fname( 'sequence.qualsolid' )
+        >>> QualityScoreSOLiD().sniff( fname )
+        True
+        """
+        try:
+            fh = open( filename )
+            readlen = None
+            goodblock = 0
+            while True:
+                line = fh.readline()
+                if not line:
+                    if goodblock > 0:
+                        return True
+                    else:
+                        break #EOF
+                line = line.strip()
+                if line and not line.startswith( '#' ): #first non-empty non-comment line
+                    if line.startswith( '>' ):
+                        line = fh.readline().strip()
+                        if line == '' or line.startswith( '>' ):
+                            break
+                        try:
+                            [ int( x ) for x in line.split() ]
+                            if not(readlen):
+                                readlen = len(line.split())
+                            assert len(line.split()) == readlen    #SOLiD reads should be of the same length
+                        except:
+                            break
+                        goodblock += 1
+                        if goodblock > 10:
+                            return True
+                    else:
+                        break #we found a non-empty line, but it's not a header
+        except:
+            pass
+        return False
+
+class QualityScore454 ( data.Text ):
+    """
+    until we know more about quality score formats
+    """
+    file_ext = "qual454"
+    
+    def set_peek( self, dataset, line_count=None ):
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek( dataset.file_name )
+            if line_count is None:
+                dataset.blurb = data.nice_size( dataset.get_size() )
+            else:
+                dataset.blurb = "%s lines, 454 Quality score file" % util.commaify( str( line_count ) )
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+    
+    def display_peek(self, dataset):
+        try:
+            return dataset.peek
+        except:
+            return "454 Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) )
+
+    def sniff( self, filename ):
+        """
+        >>> fname = get_test_fname( 'sequence.fasta' )
+        >>> QualityScore454().sniff( fname )
+        False
+        >>> fname = get_test_fname( 'sequence.qual454' )
+        >>> QualityScore454().sniff( fname )
         True
         """
         try:
@@ -63,3 +128,59 @@ class QualityScore ( data.Text ):
         except:
             pass
         return False
+
+class QualityScoreSolexa ( data.Text ):
+    """
+    until we know more about quality score formats
+    """
+    file_ext = "qualsolexa"
+    
+    def set_peek( self, dataset, line_count=None ):
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek( dataset.file_name )
+            if line_count is None:
+                dataset.blurb = data.nice_size( dataset.get_size() )
+            else:
+                dataset.blurb = "%s lines, Solexa Quality score file" % util.commaify( str( line_count ) )
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+    
+    def display_peek(self, dataset):
+        try:
+            return dataset.peek
+        except:
+            return "Solexa Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) )
+
+    def sniff( self, filename ):
+        """
+        >>> fname = get_test_fname( 'sequence.fasta' )
+        >>> QualityScoreSolexa().sniff( fname )
+        False
+        >>> fname = get_test_fname( 'sequence.qualsolexa' )
+        >>> QualityScoreSolexa().sniff( fname )
+        True
+        """
+        try:
+            fh = open( filename )
+            readlen = None
+            while True:
+                line = fh.readline()
+                if not line:
+                    break #EOF
+                line = line.strip()
+                if line and not line.startswith( '#' ):
+                    if len(line.split('\t')) > 1:
+                        break
+                    try:
+                        [ int( x ) for x in line.split() ]
+                        if not(readlen):
+                            readlen = len(line.split())
+                        assert len(line.split()) == readlen    #Solexa reads should be of the same length
+                    except:
+                        break
+                
+        except:
+            pass
+        return False
+
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 77c74d52832..f9a2b8c4072 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -116,7 +116,9 @@ class Registry( object ):
                 'laj'         : images.Laj(),
                 'lav'         : sequence.Lav(),
                 'maf'         : sequence.Maf(),
-                'qual'        : qualityscore.QualityScore(),
+                'qualsolid'   : qualityscore.QualityScoreSOLiD(),
+                'qualsolexa'  : qualityscore.QualityScoreSolexa(),
+                'qual454'     : qualityscore.QualityScore454(),
                 'scf'         : images.Scf(),
                 'tabular'     : tabular.Tabular(),
                 'taxonomy'    : tabular.Taxonomy(),
@@ -140,7 +142,9 @@ class Registry( object ):
                 'laj'         : 'text/plain',
                 'lav'         : 'text/plain',
                 'maf'         : 'text/plain',
-                'qual'        : 'text/plain',
+                'qualsolid'   : 'text/plain',
+                'qualsolexa'  : 'text/plain',
+                'qual454'     : 'text/plain',
                 'scf'         : 'application/octet-stream',
                 'tabular'     : 'text/plain',
                 'taxonomy'    : 'text/plain',
diff --git a/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py b/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
new file mode 100644
index 00000000000..1cba27320a6
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
@@ -0,0 +1,47 @@
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+import sys, logging
+
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) )
+HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True )
+        
+def upgrade():
+    # Load existing tables
+    metadata.reflect()
+    # Add 2 indexes to the galaxy_user table
+    i = Index( 'ix_hda_extension', HistoryDatasetAssociation_table.c.extension )
+    try:
+        i.create()
+    except Exception, e:
+        log.debug( "Adding index 'ix_hda_extension' to history_dataset_association table failed: %s" % ( str( e ) ) )
+
+    # Set the default data in the galaxy_user table, but only for null values
+    cmd = "UPDATE history_dataset_association SET extension = 'qual454' WHERE extension = 'qual' and peek like \'>%%\'"
+    try:
+        db_session.execute( cmd )
+    except Exception, e:
+        log.debug( "Resetting extension qual to qual454 in history_dataset_association failed: %s" % ( str( e ) ) )
+    cmd = "UPDATE history_dataset_association SET extension = 'qualsolexa' WHERE extension = 'qual' and peek not like \'>%%\'"
+    try:
+        db_session.execute( cmd )
+    except Exception, e:
+        log.debug( "Resetting extension qual to qualsolexa in history_dataset_association failed: %s" % ( str( e ) ) )
+    # Add 1 index to the history_dataset_association table
+    try:
+        i.drop()
+    except Exception, e:
+        log.debug( "Dropping index 'ix_hda_extension' to history_dataset_association table failed: %s" % ( str( e ) ) )
+
+   
+def downgrade():
+    pass
diff --git a/tools/metag_tools/fastqsolexa_to_fasta_qual.xml b/tools/metag_tools/fastqsolexa_to_fasta_qual.xml
index 5f1e5cdd9fc..6ea0d6e189d 100644
--- a/tools/metag_tools/fastqsolexa_to_fasta_qual.xml
+++ b/tools/metag_tools/fastqsolexa_to_fasta_qual.xml
@@ -6,7 +6,7 @@
   </inputs>
   <outputs>
     <data name="output1" format="fasta"/>
-    <data name="output2" format="qual"/>
+    <data name="output2" format="qualsolexa"/>
   </outputs>
   <tests>
     <!-- NOTE: this tool generates 2 output files, but our functional tests currently only handle the last one generated -->
diff --git a/tools/metag_tools/rmapq_wrapper.xml b/tools/metag_tools/rmapq_wrapper.xml
index 1447fa70259..2a02ba80c2a 100644
--- a/tools/metag_tools/rmapq_wrapper.xml
+++ b/tools/metag_tools/rmapq_wrapper.xml
@@ -13,7 +13,7 @@
 			</options>
         </param>
         <param name="input_seq" type="data" format="fasta" label="Sequence file"/>
-        <param name="input_score" type="data" format="qual" label="Quality score file"/>
+        <param name="input_score" type="data" format="qualsolexa" label="Quality score file"/>
         <param name="high_score" type="float" size="15" value="40" label="Minimum score for high-quality base (-q)"/>
         <param name="high_len" type="integer" size="15" value="36" label="Minimal high-quality bases (-M)"/>
         <param name="align_len" type="integer" size="15" value="11" label="Minimal length of a hit (-h)" help="seed"/>
@@ -46,7 +46,7 @@
         <test>
             <param name="database" value="/depot/data2/galaxy/faseq/test" />
             <param name="input_seq" value="rmapq_wrapper_test1.fasta" ftype="fasta"/>
-            <param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qual" />
+            <param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qualsolexa" />
             <param name="high_score" value="40" />
             <param name="high_len" value="36" />
             <param name="read_len" value="36" />
diff --git a/tools/metag_tools/short_reads_figure_high_quality_length.xml b/tools/metag_tools/short_reads_figure_high_quality_length.xml
index fba61acb112..d35dfb6588e 100644
--- a/tools/metag_tools/short_reads_figure_high_quality_length.xml
+++ b/tools/metag_tools/short_reads_figure_high_quality_length.xml
@@ -5,7 +5,7 @@
 
 <inputs>
 <page>
-    <param name="input1" type="data" format="qual,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
+    <param name="input1" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
     <param name="input2" type="integer" size="5" value="20" label="Quality score threshold" />
 </page>
 </inputs>
@@ -17,12 +17,12 @@
 </requirements>
 <tests>
 	<test>
-		<param name="input1" value="solexa.qual" ftype="qual" />
+		<param name="input1" value="solexa.qual" ftype="qualsolexa" />
 		<param name="input2" value="5" />
   		<output name="output1" file="solexa_high_quality_hist.pdf" ftype="pdf"/>
 	</test>
 	<test>
-		<param name="input1" value="454.qual" ftype="qual" />
+		<param name="input1" value="454.qual" ftype="qual454" />
 		<param name="input2" value="5" />
 		<output name="output1" file="454_high_quality_hist.pdf" ftype="pdf"/>
 	</test>
diff --git a/tools/metag_tools/short_reads_figure_score.xml b/tools/metag_tools/short_reads_figure_score.xml
index fc471689b6a..42f7d4602b3 100644
--- a/tools/metag_tools/short_reads_figure_score.xml
+++ b/tools/metag_tools/short_reads_figure_score.xml
@@ -5,7 +5,7 @@
 
 <inputs>
 <page>
-    <param name="input1" type="data" format="qual, txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
+    <param name="input1" type="data" format="qualsolexa, qual454, txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
 </page>
 </inputs>
 
@@ -17,11 +17,11 @@
 </requirements>
 <tests>
 	<test>
-		<param name="input1" value="solexa.qual" ftype="qual" />
+		<param name="input1" value="solexa.qual" ftype="qualsolexa" />
   		<output name="output1" file="solexaScore.png" ftype="png" />
 	</test>
 	<test>
-		<param name="input1" value="454.qual" ftype="qual" />
+		<param name="input1" value="454.qual" ftype="qual454" />
 		<output name="output1" file="454Score.png" ftype="png" />
 	</test>
 </tests>
diff --git a/tools/metag_tools/short_reads_trim_seq.xml b/tools/metag_tools/short_reads_trim_seq.xml
index 2af57f6ba39..824c022744c 100644
--- a/tools/metag_tools/short_reads_trim_seq.xml
+++ b/tools/metag_tools/short_reads_trim_seq.xml
@@ -7,7 +7,7 @@
 <inputs>
 <page>
     <param name="input1" type="data" format="fasta,txtseq.zip" label="Reads" />
-    <param name="input2" type="data" format="qual,txtseq.zip" label="Quality scores" />
+    <param name="input2" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality scores" />
 	<param name="trim" type="integer" size="5" value="20" label="Minimal quality score" help="bases scoring below this value will trigger splitting"/>
     <param name="length" type="integer" size="5" value="100" label="Minimal length of contiguous segment" help="report all high quality segments above this length. Setting this option to '0' will cause the program to return a single longest run of high quality bases per read" />
     <conditional name="sequencing_method_choice">
@@ -36,7 +36,7 @@
 	<test>
 		<param name="sequencer" value="454" />
 		<param name="input1" value="454.fasta" ftype="fasta" />
-		<param name="input2" value="454.qual" ftype="qual" />
+		<param name="input2" value="454.qual" ftype="qual454" />
 		<param name="input3" value="no" />
 		<param name="trim" value="20" />
 		<param name="length" value="0" />
@@ -45,7 +45,7 @@
 	<test>
 		<param name="sequencer" value="Solexa" />
 		<param name="input1" value="solexa.fasta" ftype="fasta" />
-		<param name="input2" value="solexa.qual" ftype="qual" />
+		<param name="input2" value="solexa.qual" ftype="qualsolexa" />
 		<param name="input3" value="0" />
 		<param name="trim" value="20" />
 		<param name="length" value="0" />