-
Notifications
You must be signed in to change notification settings - Fork 79
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #1802 from milaboratory/new-illumina-kit-dna
- added new illumina preset
- Loading branch information
Showing
4 changed files
with
349 additions
and
2 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
336 changes: 336 additions & 0 deletions
336
regression/presets/analyze/illumina-human-dna-trb-ampliseq-sr.yaml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,336 @@ | ||
| flags: [] | ||
| pipeline: | ||
| - align | ||
| - assemble | ||
| - exportClones | ||
| align: | ||
| species: hs | ||
| libraryName: default | ||
| trimmingQualityThreshold: 10 | ||
| trimmingWindowSize: 6 | ||
| chains: ALL | ||
| replaceWildcards: true | ||
| overlapPairedReads: true | ||
| bamDropNonVDJ: false | ||
| writeFailedAlignments: false | ||
| tagPattern: null | ||
| tagUnstranded: false | ||
| tagMaxBudget: 10.0 | ||
| headerExtractors: [] | ||
| readIdAsCellTag: false | ||
| sampleTable: null | ||
| tagsValidations: [] | ||
| splitBySample: true | ||
| limit: null | ||
| parameters: | ||
| vParameters: | ||
| geneFeatureToAlign: VGeneWithP | ||
| minSumScore: 150 | ||
| relativeMinScore: 0.97 | ||
| maxHits: 5 | ||
| parameters: | ||
| type: kaligner2 | ||
| mapperNValue: 8 | ||
| mapperKValue: 1 | ||
| floatingLeftBound: true | ||
| floatingRightBound: true | ||
| mapperAbsoluteMinClusterScore: 102 | ||
| mapperExtraClusterScore: -38 | ||
| mapperMatchScore: 98 | ||
| mapperMismatchScore: -14 | ||
| mapperOffsetShiftScore: -82 | ||
| mapperSlotCount: 8 | ||
| mapperMaxClusters: 11 | ||
| mapperMaxClusterIndels: 4 | ||
| mapperKMersPerPosition: 4 | ||
| mapperAbsoluteMinScore: 103 | ||
| mapperRelativeMinScore: 0.81 | ||
| mapperMinSeedsDistance: 8 | ||
| mapperMaxSeedsDistance: 8 | ||
| alignmentStopPenalty: 0 | ||
| absoluteMinScore: 150 | ||
| relativeMinScore: 0.8 | ||
| maxHits: 2 | ||
| scoring: | ||
| type: affine | ||
| alphabet: nucleotide | ||
| subsMatrix: "simple(match = 10, mismatch = -19)" | ||
| gapOpenPenalty: -62 | ||
| gapExtensionPenalty: -11 | ||
| dParameters: | ||
| geneFeatureToAlign: DRegionWithP | ||
| relativeMinScore: 0.85 | ||
| absoluteMinScore: 25.0 | ||
| maxHits: 3 | ||
| scoring: | ||
| type: linear | ||
| alphabet: nucleotide | ||
| subsMatrix: "simple(match = 5, mismatch = -9)" | ||
| gapPenalty: -12 | ||
| jParameters: | ||
| geneFeatureToAlign: JRegionWithP | ||
| minSumScore: 150 | ||
| relativeMinScore: 0.97 | ||
| maxHits: 5 | ||
| parameters: | ||
| type: kaligner2 | ||
| mapperNValue: 8 | ||
| mapperKValue: 1 | ||
| floatingLeftBound: true | ||
| floatingRightBound: true | ||
| mapperAbsoluteMinClusterScore: 102 | ||
| mapperExtraClusterScore: -38 | ||
| mapperMatchScore: 95 | ||
| mapperMismatchScore: -14 | ||
| mapperOffsetShiftScore: -82 | ||
| mapperSlotCount: 6 | ||
| mapperMaxClusters: 4 | ||
| mapperMaxClusterIndels: 4 | ||
| mapperKMersPerPosition: 4 | ||
| mapperAbsoluteMinScore: 100 | ||
| mapperRelativeMinScore: 0.8 | ||
| mapperMinSeedsDistance: 5 | ||
| mapperMaxSeedsDistance: 5 | ||
| alignmentStopPenalty: 0 | ||
| absoluteMinScore: 150 | ||
| relativeMinScore: 0.8 | ||
| maxHits: 3 | ||
| scoring: | ||
| type: affine | ||
| alphabet: nucleotide | ||
| subsMatrix: "simple(match = 10, mismatch = -19)" | ||
| gapOpenPenalty: -62 | ||
| gapExtensionPenalty: -11 | ||
| vjAlignmentOrder: VThenJ | ||
| libraryStructure: Unknown | ||
| includeDScore: false | ||
| includeCScore: false | ||
| minSumScore: 120.0 | ||
| relativeMinVFR3CDR3Score: 0.7 | ||
| allowPartialAlignments: false | ||
| allowNoCDR3PartAlignments: false | ||
| allowChimeras: false | ||
| readsLayout: DirectOnly | ||
| mergerParameters: | ||
| qualityMergingAlgorithm: MaxSubtraction | ||
| partsLayout: null | ||
| minimalOverlap: 13 | ||
| minimalMatchQualitySum: 364 | ||
| maxQuality: 50 | ||
| minimalIdentity: 0.7 | ||
| identityType: MinimalQualityWeighted | ||
| fixSeed: true | ||
| alignmentBoundaryTolerance: 5 | ||
| minChimeraDetectionScore: 120 | ||
| vjOverlapWindow: 3 | ||
| saveOriginalSequence: false | ||
| saveOriginalReads: false | ||
| smartForceEdgeAlignments: true | ||
| retriesForPartialAlignments: 3 | ||
| retriesAlignmentOfNotCoveredPart: 2 | ||
| refineTagsAndSort: | ||
| whitelists: {} | ||
| runCorrection: true | ||
| parameters: | ||
| correctionPower: 0.001 | ||
| backgroundSubstitutionRate: 0.001 | ||
| backgroundIndelRate: 1.0E-5 | ||
| minQuality: 12 | ||
| maxSubstitutions: 2 | ||
| maxIndels: 2 | ||
| maxTotalErrors: 3 | ||
| postFilter: null | ||
| assemblePartial: | ||
| overlappedOnly: false | ||
| dropPartial: false | ||
| cellLevel: false | ||
| parameters: | ||
| kValue: 12 | ||
| kOffset: -7 | ||
| minimalAssembleOverlap: 12 | ||
| minimalNOverlap: 7 | ||
| minimalNOverlapShare: 0.65 | ||
| minimalAlignmentMergeIdentity: 0.85 | ||
| mergerParameters: | ||
| qualityMergingAlgorithm: SumSubtraction | ||
| partsLayout: CollinearDirect | ||
| minimalOverlap: 20 | ||
| minimalMatchQualitySum: 0 | ||
| maxQuality: 45 | ||
| minimalIdentity: 0.95 | ||
| identityType: Unweighted | ||
| maxLeftParts: 256000 | ||
| maxLeftMatches: 6144 | ||
| extend: | ||
| vAnchor: CDR3Begin | ||
| jAnchor: FR4Begin | ||
| minimalVScore: 50 | ||
| minimalJScore: 50 | ||
| assemble: | ||
| sortBySequence: false | ||
| clnaOutput: false | ||
| cellLevel: false | ||
| consensusAssemblerParameters: null | ||
| cloneAssemblerParameters: | ||
| assemblingFeatures: | ||
| - CDR3 | ||
| minimalClonalSequenceLength: 12 | ||
| qualityAggregationType: BetaScore | ||
| cloneClusteringParameters: | ||
| searchDepth: 2 | ||
| allowedMutationsInNRegions: 1 | ||
| searchParameters: twoMismatchesOrIndels | ||
| clusteringFilter: | ||
| type: advanced | ||
| correctionPower: 0.001 | ||
| backgroundSubstitutionRate: 0.002 | ||
| backgroundIndelRate: 2.0E-4 | ||
| cloneFactoryParameters: | ||
| vParameters: | ||
| maxAlignmentWidthLinear: 5 | ||
| maxAlignmentWidthAffine: 500 | ||
| jParameters: | ||
| maxAlignmentWidthLinear: 5 | ||
| maxAlignmentWidthAffine: 500 | ||
| cParameters: | ||
| maxAlignmentWidthLinear: 5 | ||
| maxAlignmentWidthAffine: 500 | ||
| dParameters: | ||
| relativeMinScore: null | ||
| absoluteMinScore: null | ||
| maxHits: null | ||
| scoring: null | ||
| separateByV: false | ||
| separateByJ: false | ||
| separateByC: false | ||
| maximalPreClusteringRatio: 1.0 | ||
| preClusteringScoreFilteringRatio: 2.0 | ||
| preClusteringCountFilteringRatio: 2.0 | ||
| addReadsCountOnClustering: false | ||
| badQualityThreshold: 15 | ||
| maxBadPointsPercent: 0.7 | ||
| mappingThreshold: 2of5 | ||
| minimalQuality: 20 | ||
| postFilters: null | ||
| inferMinRecordsPerConsensus: false | ||
| assembleContigs: | ||
| ignoreTags: false | ||
| parameters: | ||
| branchingMinimalQualityShare: 0.1 | ||
| branchingMinimalSumQuality: 60 | ||
| decisiveBranchingSumQualityThreshold: 120 | ||
| alignedSequenceEdgeDelta: 3 | ||
| alignmentEdgeRegionSize: 7 | ||
| minimalNonEdgePointsFraction: 0.25 | ||
| minimalMeanNormalizedQuality: 5.0 | ||
| outputMinimalQualityShare: 0.75 | ||
| outputMinimalSumQuality: 0 | ||
| subCloningRegions: null | ||
| assemblingRegions: null | ||
| postFiltering: | ||
| type: NoFiltering | ||
| trimmingParameters: | ||
| averageQualityThreshold: 10.0 | ||
| windowSize: 8 | ||
| minimalContigLength: 20 | ||
| alignedRegionsOnly: false | ||
| discardAmbiguousNucleotideCalls: false | ||
| cloneFactoryParameters: | ||
| vParameters: | ||
| relativeMinScore: 0.97 | ||
| maxAlignmentWidthLinear: 5 | ||
| maxAlignmentWidthAffine: 500 | ||
| jParameters: | ||
| maxAlignmentWidthLinear: 5 | ||
| maxAlignmentWidthAffine: 500 | ||
| cParameters: | ||
| maxAlignmentWidthLinear: 5 | ||
| maxAlignmentWidthAffine: 500 | ||
| dParameters: | ||
| relativeMinScore: null | ||
| absoluteMinScore: null | ||
| maxHits: null | ||
| scoring: null | ||
| exportAlignments: | ||
| chains: ALL | ||
| noHeader: false | ||
| fields: | ||
| - field: -readIds | ||
| - field: -targetSequences | ||
| - field: -targetQualities | ||
| - field: -vHitsWithScore | ||
| - field: -dHitsWithScore | ||
| - field: -jHitsWithScore | ||
| - field: -cHitsWithScore | ||
| - field: -vAlignments | ||
| - field: -dAlignments | ||
| - field: -jAlignments | ||
| - field: -cAlignments | ||
| - field: -allNFeaturesWithMinQuality | ||
| - field: -allAAFeatures | ||
| - field: -defaultAnchorPoints | ||
| - field: -topChains | ||
| exportClones: | ||
| splitByTagType: null | ||
| filterOutOfFrames: false | ||
| filterStops: false | ||
| chains: ALL | ||
| noHeader: false | ||
| fields: | ||
| - field: -cloneId | ||
| - field: -readCount | ||
| - field: -readFraction | ||
| - field: -targetSequences | ||
| - field: -targetQualities | ||
| - field: -vHitsWithScore | ||
| - field: -dHitsWithScore | ||
| - field: -jHitsWithScore | ||
| - field: -cHitsWithScore | ||
| - field: -vAlignments | ||
| - field: -dAlignments | ||
| - field: -jAlignments | ||
| - field: -cAlignments | ||
| - field: -allNFeaturesWithMinQuality | ||
| - field: -allAAFeatures | ||
| - field: -defaultAnchorPoints | ||
| splitFilesBy: | ||
| - chain | ||
| groupClonesBy: [] | ||
| qc: | ||
| checks: | ||
| - type: SuccessfullyAlignedReads | ||
| upper: 0.85 | ||
| middle: 0.7 | ||
| label: Successfully aligned reads | ||
| - type: OffTargetReads | ||
| upper: 0.2 | ||
| middle: 0.1 | ||
| label: Off target (non TCR/IG) reads | ||
| - type: ReadsWithNoVOrJHits | ||
| upper: 0.2 | ||
| middle: 0.1 | ||
| label: Reads with no V or J hits | ||
| - type: ReadsUsedInClonotypes | ||
| upper: 0.9 | ||
| middle: 0.7 | ||
| label: Reads used in clonotypes | ||
| - type: AlignmentsWithNoAssemblingFeature | ||
| upper: 0.15 | ||
| middle: 0.05 | ||
| label: Alignments without assembling feature | ||
| - type: AlignmentsDroppedLowQuality | ||
| upper: 0.05 | ||
| middle: 0.01 | ||
| label: Alignments dropped due to low sequence quality | ||
| - type: ClonesDroppedInPostFiltering | ||
| upper: 0.05 | ||
| middle: 0.01 | ||
| label: Clones dropped in post-filtering | ||
| - type: AlignmentsDroppedInPostFiltering | ||
| upper: 0.05 | ||
| middle: 0.01 | ||
| label: Alignments dropped in clones post-filtering | ||
| - type: OverlappedReadsMoreBetter | ||
| upper: 0.9 | ||
| middle: 0.8 | ||
| label: Overlapped paired-end reads |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters