diff --git a/src/main/resources/gridss.properties b/src/main/resources/gridss.properties index bec4adc89..89c54d7ba 100644 --- a/src/main/resources/gridss.properties +++ b/src/main/resources/gridss.properties @@ -1,5 +1,5 @@ -maxCoverage = 10000 -minMapq = 10 +maxCoverage = 25000 +minMapq = 20 fallbackMapq = 20 #maxMapq = 70 minAnchorShannonEntropy = 0.5 @@ -47,12 +47,12 @@ assembly.errorCorrection.maxBaseMismatchForCollapse = 2 assembly.errorCorrection.maxPathCollapseLengthMultiple = 2.0 assembly.realignContigs = true assembly.downsample.acceptDensityPortion = 0.5 -assembly.downsample.targetEvidenceDensity = 5.0 +assembly.downsample.targetEvidenceDensity = 6.0 assembly.downsample.minimumDensityWindowSize = 1000 assembly.positional.maxPathLengthMultiple = 1.1 assembly.positional.retainWidthMultiple = 5.0 assembly.positional.flushWidthMultiple = 10.0 -assembly.positional.maximumNodeDensity = 5.0 +assembly.positional.maximumNodeDensity = 2.0 assembly.positional.trimSelfIntersectingReads = true assembly.positional.forceFullMemoizationRecalculationAt = 0.8