SequencerRunQcChecker

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of SequencerRunQcChecker for Sequencer Run QC Checker.

Domain limits and critical parameters

• Performs instrument-level run QC per CAP/CLIA §GEN.48800, ISO 15189 §7.3.4, FDA NGS guidance and manufacturer specifications: clustering/loading metrics (cluster density within range, PF% ≥75%, phasing/prephasing ≤1.0%, occupancy ≥70% for patterned FCs), base quality (Q30 R1/R2 ≥75%, Q40 for newer chemistries, quality drop cycle detection), output metrics (yield ≥80% expected, alignment rate ≥70%), controls (PhiX error rate ≤2.0%, spike-in passed, negative control clean), flow cell uniformity (l
• ⚠️ Critical: PhiX error rate is the most sensitive early indicator of sequencing problems. Overclustering irreversibly degrades quality; underloading preferred over overloading. Expired consumables = legally invalid data for clinical use. Fluidics issues manifest as high phasing + lane non-uniformity. Index hopping on patterned FCs without UDI can reach 5–10%. Quality drop at specific cycle indicates nucleotide or chemistry cycle issue. Temperature instability affects polymerase kinetics and red
• ⚠️ Note: This utility assesses SEQUENCER INSTRUMENT-LEVEL RUN QUALITY. It does not replace sample/library-level QC (LibraryPrepBatchChecker, PanelCoverageQcChecker) or bioinformatic variant validation. All three levels are required: instrument QC → library/sample QC → bioinformatic QC. Data from FAIL runs must not enter the bioinformatics pipeline until the issue is resolved or the run is repeated.

URS — User Requirements Specification

input.csv contract

RunID,Platform,InstrumentSerial,FlowCell_Type,Chemistry_Version,ReadConfiguration,RunStartDate,RunEndDate,RunDuration_Hours,ClusterDensity_K_mm2,MinClusterDensity_K_mm2,MaxClusterDensity_K_mm2,PercentPF,MinPercentPF,PhasingRate_Percent,MaxPhasingRate_Percent,PrephasingRate_Percent,MaxPrephasingRate_Percent,Occupancy_Percent,MinOccupancy_Percent,PercentQ30_Read1,PercentQ30_Read2,PercentQ30_Index1,PercentQ30_Index2,MinPercentQ30,PercentQ40_Read1,MedianQualityScore,QualityDrop_Cycle,TotalReads_Million,ExpectedReads_Million,Yield_Gb,ExpectedYield_Gb,PercentAligned,MinPercentAligned,PhiX_ErrorRate_Percent,MaxPhiX_ErrorRate_Percent,PhiX_AlignmentRate_Percent,SpikeIn_Control_Passed,NegativeControl_Clean,LaneUniformity_CV_Percent,MaxLaneUniformity_CV_Percent,TileHotspots_Detected,IndexHopping_Rate_Percent,MaxIndexHopping_Rate_Percent,Calibration_Current,Maintenance_UpToDate,ErrorCodes_DuringRun,FluidicsIssues_Detected,OpticsIssues_Detected,TemperatureStability_CV,MaxTemperatureStability_CV,ReagentKit_Lot,FlowCell_Lot,Consumables_Expired,ReagentKit_RemainingCycles
NS6000-2026-0142,NovaSeq_6000,A01234,S4,v1.5,2x150,2026-06-07T08:00:00,2026-06-08T04:00:00,20,950,600,1200,88.5,75,0.15,1.0,0.12,1.0,92.0,70,92.5,89.8,95.2,94.8,75,78.5,36,0,2800,3000,840,900,96.5,70,0.18,2.0,98.5,true,true,4.2,15,false,0.03,0.5,true,true,,false,false,0.08,0.5,RK-2026-0451,FC-2026-0892,false,0
NS6000-2026-0143,NovaSeq_6000,A01234,SP,v1.5,2x100,2026-06-08T10:00:00,2026-06-08T22:00:00,12,1350,600,1200,58.0,75,2.8,1.0,1.9,1.0,95.0,70,68.5,55.2,82.0,78.5,75,35.0,28,45,450,800,90,160,72.0,70,3.5,2.0,92.0,false,true,22.5,15,true,1.8,0.5,true,false,ERR_FLUIDICS_BUBBLE;ERR_TEMP_SPIKE,true,false,0.85,0.5,RK-2026-0467,FC-2026-0901,false,0

Input validation rules

FS — Functional Specification

Example output.json

{
  "utilityId": "sequencerrunqcchecker",
  "utilityFolder": "SequencerRunQcChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "RunID",
      "value": "NS6000-2026-0142",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "Platform",
      "value": "NovaSeq_6000",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "InstrumentSerial",
      "value": "A01234",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "FlowCell_Type",
      "value": "S4",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "Chemistry_Version",
      "value": "v1.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "ReadConfiguration",
      "value": "2x150",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "RunStartDate",
      "value": "2026-06-07T08:00:00",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "RunEndDate",
      "value": "2026-06-08T04:00:00",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "RunDuration_Hours",
      "value": "20",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "ClusterDensity_K_mm2",
      "value": "950",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "MinClusterDensity_K_mm2",
      "value": "600",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "MaxClusterDensity_K_mm2",
      "value": "1200",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-012"
    }
  ],
  "criticalFindings": [],
  "warnings": [],
  "audit": {
    "inputHash": "sha256:<calculated at runtime>",
    "rulesVersion": "<utility executable version>",
    "documentation": "SequencerRunQcChecker.documentation.html"
  }
}

Traceability matrix

IQ/OQ/PQ test scenarios

QA/QC and change control

• Do not rename columns without updating validator, documentation and test set.
• Retain input.csv, output.json, executable version and checksum.
• Before production use, perform IQ/OQ/PQ or equivalent CSV/CSA verification.
• Critical limits shall be verified against the approved specification, registration dossier and local SOPs.
• The utility provides structured QC decision support; final release decision remains with QA/QP and approved procedures.