preset for bruker v2

milaboratory · Oct 31, 2024 · dac58df · dac58df
1 parent 3956c95
commit dac58df
Showing 1 changed file with 24 additions and 25 deletions.
diff --git a/src/main/resources/presets/protocols/bruker.yaml b/src/main/resources/presets/protocols/bruker.yaml
@@ -24,6 +24,9 @@
   mitool:
     parse:
       inheritFrom: mitool-parse-default
+      overrides:
+        trimmingQualityThreshold: 20
+        trimmingWindowSize: 5
     refineTags:
       inheritFrom: mitool-refineTags-default
       overrides:
@@ -44,32 +47,28 @@
             - ACTACTTCTG
             - GCCTTGTTGT
     consensus:
-      inheritFrom: mitool-consensus-2-steps
+      inheritFrom: mitool-consensus-1-steps
       overrides:
-        - groupingTagTypes:
-            - Cell
-          payloadTagTypes:
-            - Targets
-          parameters:
-            aAssemblerParameters:
-              minAlignmentScore: 80
-              maxNormalizedAlignmentPenalty: 0.13
-            positiveMinQualityShare: 0.13
-            positiveMinIntersectionQuality: 150
-            minRecordSharePerConsensus: 0.001
-            minRecordsPerConsensus: 3
-        - groupingTagTypes:
-            - Cell
-          payloadTagTypes:
-            - Targets
-          parameters:
-            aAssemblerParameters:
-              minAlignmentScore: 71
-              maxNormalizedAlignmentPenalty: 0.1
-            positiveMinQualityShare: 0.14
-            positiveMinIntersectionQuality: 239
-            minRecordSharePerConsensus: 1.0
-            minRecordsPerConsensus: 3
+        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
   align:
     inheritFrom: align-single-cell
     overrides: