# Work Instruction: [Title]

| Document ID | WI-001 |
|-------------|--------|
| Title | [Title] |
| Revision | 1.0 |
| Effective Date | [DATE] |
| Author | [AUTHOR] |
| Approved By | [APPROVER] |
| Department | Genetics & Genomics Laboratory |

---

## 1. Purpose

[Describe the purpose of this work instruction - e.g., NGS library preparation, variant calling, DNA extraction]

## 2. Scope

[Define what activities this instruction covers - e.g., specific assay, platform, sample types]

## 3. Safety Precautions

- [List any safety requirements - biological hazards, chemical reagents]
- [Personal protective equipment needed - lab coat, gloves, eye protection]
- [Hazards to be aware of - ethidium bromide, formamide, liquid nitrogen]
- [Biosafety level requirements]

## 4. Equipment/Materials Required

| Item | Specification | Vendor/Catalog # |
|------|---------------|------------------|
| [Sequencing Platform] | [Model/Version] | [Vendor] |
| [Reagent Kit] | [Kit Name/Version] | [Catalog #] |
| [Software] | [Version] | [Source] |
| | | |

## 5. Quality Control Materials

| QC Material | Purpose | Acceptance Criteria |
|-------------|---------|---------------------|
| [Positive Control] | [Purpose] | [Criteria] |
| [Negative Control] | [Purpose] | [Criteria] |
| [Reference Standard] | [Purpose] | [Criteria] |

## 6. Pre-Procedure Setup

### 6.1 Sample Verification
[Steps to verify sample identity, labeling, and chain of custody]

### 6.2 Equipment Preparation
[Equipment calibration, cleaning, initialization steps]

### 6.3 Reagent Preparation
[Reagent thawing, mixing, QC verification]

## 7. Procedure

### Step 1: [Title]
[Detailed instructions with specific parameters]
- [Sub-step with settings/values]
- [Expected outcome/checkpoint]

### Step 2: [Title]
[Detailed instructions]
- [Sub-step]
- [Expected outcome/checkpoint]

### Step 3: [Title]
[Detailed instructions]
- [Sub-step]
- [Expected outcome/checkpoint]

## 8. Quality Metrics

| Metric | Target Value | Action if Out of Spec |
|--------|--------------|----------------------|
| [Coverage Depth] | [>20x for germline] | [Repeat sequencing] |
| [Q30 Score] | [>80%] | [Investigate/rerun] |
| [Uniformity] | [>0.8] | [Troubleshoot] |
| [Contamination] | [<3%] | [Reject sample] |

## 9. Acceptance Criteria

[Define what constitutes successful completion]
- [Criteria 1 with specific threshold]
- [Criteria 2 with specific threshold]
- [Criteria 3 with specific threshold]

## 10. Troubleshooting

| Problem | Possible Cause | Solution |
|---------|----------------|----------|
| [Issue] | [Cause] | [Action] |
| [Issue] | [Cause] | [Action] |

## 11. Records

| Record | Location | Retention Period |
|--------|----------|------------------|
| [Run Log] | [LIMS/Path] | [CAP requirement] |
| [QC Results] | [LIMS/Path] | [Minimum 2 years] |
| [Variant Call Files] | [Secure Storage] | [Per CLIA/CAP] |

## 12. Data Management

- [File naming conventions]
- [Data backup procedures]
- [Version control for pipelines/software]
- [Data retention and archival]

## 13. References

### Related SOPs
- [SOP-SEQ-XXX: NGS Quality Control]
- [SOP-DM-XXX: Bioinformatics Data Management]
- [SOP-GEN-XXX: Sample Tracking]

### Manufacturer Documentation
- [Instrument User Guide, Version X]
- [Reagent Kit Insert, Version X]
- [Software Manual, Version X]

### Standards and Guidelines
- [CAP Molecular Pathology Checklist]
- [CLIA requirements]
- [Relevant professional guidelines]

---

## Revision History

| Rev | Date | Description | Author |
|-----|------|-------------|--------|
| 1.0 | [DATE] | Initial release | [AUTHOR] |