bruker consensus correction

milaboratory · Oct 31, 2024 · a07d30a · a07d30a
1 parent d1714a9
commit a07d30a
Showing 1 changed file with 33 additions and 22 deletions.
diff --git a/src/main/resources/presets/protocols/bruker.yaml b/src/main/resources/presets/protocols/bruker.yaml
@@ -47,28 +47,39 @@
             - ACTACTTCTG
             - GCCTTGTTGT
     consensus:
-      inheritFrom: mitool-consensus-1-steps
-      overrides:
-        groupingTagTypes:
-          - Cell
-        payloadTagTypes:
-          - Targets
-        parameters:
-          maxIterationsPerConsensus: 90
-          useWeightsForRecordsPerConsensus: false
-          aAssemblerParameters:
-            bandWidth: 4
-            scoring:
-              alphabet: nucleotide
-              subsMatrix: "simple(match = 5, mismatch = -10)"
-              gapPenalty: -19
-            minAlignmentScore: 60
-            maxNormalizedAlignmentPenalty: 0.4
-          positiveMinQualityShare: 0.21
-          positiveMinIntersectionQuality: 238
-          minRecordSharePerConsensus: 0.01
-          minRecordsPerConsensus: 0
-          maxConsensuses: 0
+      groupingTagTypes:
+        - Cell
+      payloadTagTypes:
+        - Targets
+      parameters:
+        aAssemblerParameters:
+          bandWidth: 4
+          scoring:
+            type: linear
+            alphabet: nucleotide
+            subsMatrix: "simple(match = 5, mismatch = -10)"
+            gapPenalty: -19
+          minAlignmentScore: 60
+          maxNormalizedAlignmentPenalty: 0.4
+          trimMinimalSumQuality: 0
+          trimReferenceRegion: true
+          maxQuality: 45
+        kMapParameters:
+          k: 9
+          useQ1Score: true
+          coreSequenceKMers: 20
+          coreSequenceRecordScore: 20
+          neighbourhoodSize: 2
+        positiveMinQualityShare: 0.21
+        positiveMinIntersectionQuality: 238
+        minAlignmentScoreForDiscardRecord: 0
+        maxNormalizedAlignmentPenaltyForDiscardRecord: 0.0
+        minRecordSharePerConsensus: 0.01
+        minRecordsPerConsensus: 0
+        useWeightsForRecordsPerConsensus: false
+        minRecordWeightForUse: 0
+        maxIterationsPerConsensus: 90
+        maxConsensuses: 0
   align:
     inheritFrom: align-single-cell
     overrides: