diff --git a/scripts/partitioning.sh b/scripts/partitioning.sh
new file mode 100644
index 0000000..0902a56
--- /dev/null
+++ b/scripts/partitioning.sh
@@ -0,0 +1,63 @@
+#!/bin/bash
+
+PAF=$1
+FASTA_FAI=$2
+AVG_WINDOW_SIZE=$3
+SAMPLE=$4
+
+grep $SAMPLE $FASTA_FAI -w -m 1 | awk -v OFS='\t' '{print($1,"0",$2)}' > $SAMPLE.bed
+bedtools makewindows -b $SAMPLE.bed -w $AVG_WINDOW_SIZE > windows.bed
+
+MASK_BED=mask.bed
+touch $MASK_BED
+
+MISSING_BED=missing.bed
+cut -f 1,2 $PAF | sort | uniq | awk -v OFS='\t' '{print($1,"0",$2,".",".","+")}' > $MISSING_BED
+
+num=0
+while [ -s windows.bed ]; do
+    echo "Processing new window set..."
+
+    cat windows.bed | while read REGION; do
+        REGION2=$(echo $REGION | sed 's/\t/:/' | sed 's/\t/-/')
+        echo Partition $num - $REGION
+
+        # Get partition
+        impg -p $PAF -r $REGION2 -x | bedtools sort | bedtools merge -s -c 4,5,6 -o distinct > partition$num.tmp.bed
+
+        # Apply mask
+        bedtools subtract -a partition$num.tmp.bed -b $MASK_BED -s > partition$num.bed
+
+        # Update mask
+        cat partition$num.bed $MASK_BED | bedtools sort > $num.bed
+        bedtools merge -i $num.bed -s -c 4,5,6 -o distinct > $num.mask.bed
+        cp $num.mask.bed $MASK_BED
+
+        # Update missing
+        bedtools subtract -a $MISSING_BED -b partition$num.bed -s > $num.missing.bed
+        cp $num.missing.bed $MISSING_BED
+
+        # Cleanup
+        rm partition$num.tmp.bed $num.bed $num.merge.bed $num.missing.bed
+
+        num=$((num + 1))
+    done
+
+    # Check if there are any missing regions not covered by mask
+    bedtools subtract -a $MISSING_BED -b $MASK_BED -s > $num.remaining.bed
+    
+    if [ ! -s $num.remaining.bed ]; then
+        # If no remaining regions, we're done
+        ###rm $num.remaining.bed
+        break
+    fi
+
+    # Take longest missing range and create new windows
+    awk -v OFS='\t' '{print($0,$3-$2)}' $num.remaining.bed | sort -k 7,7nr | cut -f 1-6 | head -n 1 > $num.new.bed
+    bedtools makewindows -b $num.new.bed -w $AVG_WINDOW_SIZE > windows.bed
+    
+    # Cleanup
+    rm $num.remaining.bed $num.new.bed
+done
+
+rm windows.bed