diff --git a/pkg/obichunk/chunk.go b/pkg/obichunk/chunk.go
index 644349b..6eff757 100644
--- a/pkg/obichunk/chunk.go
+++ b/pkg/obichunk/chunk.go
@@ -11,11 +11,12 @@ func ISequenceChunk(iterator obiiter.IBioSequence,
 	dereplicate bool,
 	na string,
 	statsOn obiseq.StatsOnDescriptions,
+	uniqueClassifier *obiseq.BioSequenceClassifier,
 ) (obiiter.IBioSequence, error) {
 
 	if onMemory {
 		return ISequenceChunkOnMemory(iterator, classifier)
 	} else {
-		return ISequenceChunkOnDisk(iterator, classifier, dereplicate, na, statsOn)
+		return ISequenceChunkOnDisk(iterator, classifier, dereplicate, na, statsOn, uniqueClassifier)
 	}
 }
diff --git a/pkg/obichunk/chunk_on_disk.go b/pkg/obichunk/chunk_on_disk.go
index dd678f9..2877beb 100644
--- a/pkg/obichunk/chunk_on_disk.go
+++ b/pkg/obichunk/chunk_on_disk.go
@@ -78,6 +78,7 @@ func ISequenceChunkOnDisk(iterator obiiter.IBioSequence,
 	dereplicate bool,
 	na string,
 	statsOn obiseq.StatsOnDescriptions,
+	uniqueClassifier *obiseq.BioSequenceClassifier,
 ) (obiiter.IBioSequence, error) {
 	obiutils.RegisterAPipe()
 	dir, err := tempDir()
@@ -120,18 +121,21 @@ func ISequenceChunkOnDisk(iterator obiiter.IBioSequence,
 			if dereplicate {
 				u := make(map[string]*obiseq.BioSequence)
 				var source string
+				uniqueClassifier.Reset()
 
 				for iseq.Next() {
 					batch := iseq.Get()
 					source = batch.Source()
 
 					for _, seq := range batch.Slice() {
-						sstring := seq.String()
-						prev, ok := u[sstring]
+						// Use composite key: sequence + categories
+						code := uniqueClassifier.Code(seq)
+						key := uniqueClassifier.Value(code)
+						prev, ok := u[key]
 						if ok {
 							prev.Merge(seq, na, true, statsOn)
 						} else {
-							u[sstring] = seq
+							u[key] = seq
 						}
 					}
 				}
diff --git a/pkg/obichunk/unique.go b/pkg/obichunk/unique.go
index ba8cc4a..b5297d6 100644
--- a/pkg/obichunk/unique.go
+++ b/pkg/obichunk/unique.go
@@ -28,29 +28,32 @@ func IUniqueSequence(iterator obiiter.IBioSequence,
 	cat := opts.Categories()
 	na := opts.NAValue()
 
-	var classifier *obiseq.BioSequenceClassifier
+	// Classifier for bucketing: Hash only to control number of chunks
+	bucketClassifier := obiseq.HashClassifier(opts.BatchCount())
 
+	// Classifier for uniqueness: Sequence + categories
+	var uniqueClassifier *obiseq.BioSequenceClassifier
 	if len(cat) > 0 {
 		cls := make([]*obiseq.BioSequenceClassifier, len(cat)+1)
+		cls[0] = obiseq.SequenceClassifier()
 		for i, c := range cat {
 			cls[i+1] = obiseq.AnnotationClassifier(c, na)
 		}
-		cls[0] = obiseq.HashClassifier(opts.BatchCount())
-		classifier = obiseq.CompositeClassifier(cls...)
+		uniqueClassifier = obiseq.CompositeClassifier(cls...)
 	} else {
-		classifier = obiseq.HashClassifier(opts.BatchCount())
+		uniqueClassifier = obiseq.SequenceClassifier()
 	}
 
 	if opts.SortOnDisk() {
 		nworkers = 1
-		iterator, err = ISequenceChunkOnDisk(iterator, classifier, true, na, opts.StatsOn())
+		iterator, err = ISequenceChunkOnDisk(iterator, bucketClassifier, true, na, opts.StatsOn(), uniqueClassifier)
 
 		if err != nil {
 			return obiiter.NilIBioSequence, err
 		}
 
 	} else {
-		iterator, err = ISequenceChunkOnMemory(iterator, classifier)
+		iterator, err = ISequenceChunkOnMemory(iterator, bucketClassifier)
 
 		if err != nil {
 			return obiiter.NilIBioSequence, err
@@ -93,9 +96,9 @@ func IUniqueSequence(iterator obiiter.IBioSequence,
 	}
 
 	for i := 0; i < nworkers-1; i++ {
-		go ff(iterator.Split(), obiseq.SequenceClassifier())
+		go ff(iterator.Split(), uniqueClassifier.Clone())
 	}
-	go ff(iterator, obiseq.SequenceClassifier())
+	go ff(iterator, uniqueClassifier)
 
 	iMerged := iUnique.IMergeSequenceBatch(opts.NAValue(),
 		opts.StatsOn(),
diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go
index 4a91c52..7e2201e 100644
--- a/pkg/obioptions/version.go
+++ b/pkg/obioptions/version.go
@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "f55dd55"
+var _Commit = "52244cd"
 var _Version = "Release 4.4.0"
 
 // Version returns the version of the obitools package.