Jun 15, 2026
Version 3
Sample-to-report traceability checklist for viral NGS workflows V.3
- 1National Institute of Health, Islamabad, Pakistan
- Public-Safe Viral Genomics Workflow Checklists
Protocol Citation: Syed Adnan Haider 2026. Sample-to-report traceability checklist for viral NGS workflows. protocols.io https://dx.doi.org/10.17504/protocols.io.3byl4meb8lo5/v3Version created by Syed Adnan Haider
Manuscript citation:
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: June 13, 2026
Last Modified: June 15, 2026
Protocol Integer ID: 319106
Keywords: viral genomics, NGS, sample-to-report, traceability, quality systems, QC, public health, workflow implementation, bioinformatics, reporting, traceability checklist for viral ng, traceability checklist, reviewing traceability, viral ng, molecular surveillance, reproducible workflow implementation, sequencing workflow, reportability decision, health genomic, pipeline versioning, laboratory quality, diagnostic policy, safe review framework, qc summary, checklist, traceability, workflow, viral
Disclaimer
This protocol is a public-safe checklist and review framework for training, documentation, and reproducible workflow demonstration. It does not replace locally approved SOPs, diagnostic policies, validation records, biosafety procedures, or institutional reporting approval. It does not include restricted sample identifiers, raw sequence data, patient information, exact surveillance locations, internal SOP text, operational wet-lab parameters, primer sequences, reagent volumes, incubation conditions, instrument recipes, credentials, or confidential partner records.
Abstract
This checklist provides a structured framework for reviewing traceability across viral next-generation sequencing workflows. It links sample/run documentation, control review, pipeline versioning, QC summaries, interpretation status, reportability decisions, and handover records. The checklist is intended for public-health genomics, molecular surveillance, training, portfolio documentation, and reproducible workflow implementation. It is a public-safe review framework and does not replace locally approved SOPs, diagnostic policies, or laboratory quality-system records.
Guidelines
Version: 0.1.0
Protocol type: Checklist / public-safe workflow review framework
Short description: A public-safe checklist for documenting how viral NGS results are traced from sample and run records through QC review, interpretation, reportability, release, and handover.
Purpose: The purpose of this checklist is to document whether a viral NGS workflow has a clear traceability path from initial sample/run records to final reporting and handover. The checklist helps reviewers confirm that a result is not only generated, but also linked to the records, controls, QC evidence, analysis version, interpretation status, and reviewer decision that support it.
Scope: This checklist can be used for Illumina, Oxford Nanopore, Ion Torrent, amplicon, metagenomic, or hybrid viral genomics workflows. It is suitable for public-safe training materials, synthetic examples, redacted portfolio documentation, protocols.io records, GitHub repositories, and supervisor-facing evidence packages. This checklist is not a diagnostic method, laboratory SOP, formal validation protocol, or substitute for local quality-management procedures.
Intended users:
- Viral genomics analysts
- Public-health laboratory teams
- Bioinformatics trainees
- Laboratory supervisors
- Project collaborators
- Reviewers assessing workflow implementation and quality documentation
Materials
No biological materials are required. This checklist uses documentation artifacts only: synthetic or redacted sample maps, run records, control summaries, QC tables, interpretation summaries, report status tables, and handover notes.
Safety warnings
This checklist is a public-safe traceability framework. It does not include restricted sample identifiers, raw sequence data, exact surveillance locations, patient information, credentials, internal SOP text, primer sequences, reagent volumes, incubation conditions, instrument recipes, local diagnostic thresholds, or controlled institutional records.
Before start
Confirm that all example identifiers are synthetic, redacted, or approved for public release. Do not include restricted sample IDs, patient information, raw sequence files, exact locations, internal SOP text, credentials, or operational wet-lab parameters.
Procedure
Confirm protocol metadata and public-safe status: Record the protocol title, version, intended use, author, and public-safe status before completing the checklist.
[ ] Title and version are recorded.
[ ] Protocol type and intended use are clear.
[ ] Public-safe, synthetic, redacted, or approved public status is confirmed.
Review required inputs: Confirm that the documentation artifacts needed for this review are available and internally consistent.
[ ] Synthetic or redacted sample/run map
[ ] Sequencing batch or run record
[ ] Control layout summary
[ ] Pipeline name and version
[ ] QC summary table
[ ] Coverage, consensus, or classification status table
[ ] Interpretation summary
[ ] Report or handover status record
[ ] Reviewer or release record
Define expected outputs: Confirm which review outputs, decision logs, summaries, or handover records should be produced.
[ ] Completed traceability checklist
[ ] Sample/run status table
[ ] Public-safe decision log
[ ] Handover-ready summary
[ ] List of restricted fields excluded from public release
Administrative traceability: Complete the administrative traceability review and record unresolved issues before release or handover.
[ ] Workflow title and intended use are recorded.
[ ] Analyst and reviewer roles are recorded according to local policy.
[ ] Analysis date and review date are recorded.
[ ] Approved local method, SOP, or project reference is cited without copying controlled internal text.
[ ] Public example status is marked as synthetic, redacted, or approved public data.
[ ] Version, release tag, or repository location is recorded where applicable.
Sample and run traceability: Complete the sample and run traceability review and record unresolved issues before release or handover.
[ ] Sample identifiers are synthetic, redacted, or approved for public release.
[ ] Run or batch identifiers are recorded in a non-sensitive form.
[ ] Sample sheet, barcode/index map, and output names are internally consistent.
[ ] Controls are distinguishable from samples.
[ ] Missing, duplicated, unexpected, or excluded records are documented.
[ ] Exact site, patient, household, or restricted surveillance identifiers are absent from public copies.
Analysis traceability: Complete the analysis traceability review and record unresolved issues before release or handover.
[ ] Pipeline or analysis workflow name is recorded.
[ ] Pipeline version, release tag, commit, container, or environment version is recorded.
[ ] Reference set or database version is described at a high level.
[ ] Input, output, log, and report folders are internally linkable.
[ ] Public examples use safe file names and synthetic paths.
[ ] Any manual step or external review is recorded with a short rationale.
QC and decision traceability: Complete the qc and decision traceability review and record unresolved issues before release or handover.
[ ] Run-level QC status is recorded.
[ ] Control status is reviewed before sample interpretation.
[ ] Read yield, depth, breadth, ambiguity, consensus, or classification status is recorded where relevant.
[ ] Interpretation status is assigned using controlled categories.
[ ] Repeat, manual-review, hold, or not-reportable decisions include a short reason.
[ ] Reviewer status is recorded before report release.
Reporting and handover traceability: Complete the reporting and handover traceability review and record unresolved issues before release or handover.
[ ] Final report, dashboard, table, or handover status is recorded.
[ ] Public-health caveats are included where evidence is partial or uncertain.
[ ] Submission status to public databases is recorded if applicable.
[ ] Handover notes identify what another analyst needs to reproduce the review.
[ ] Public-safe outputs are separated from restricted operational records.
[ ] Archive location, release version, or DOI is added only after it exists.
Public-safe release review: Complete the public-safe release review and record unresolved issues before release or handover.
[ ] Restricted metadata are removed or generalized.
[ ] Raw restricted sequence files are not attached.
[ ] Internal SOP text is not copied.
[ ] Credentials, server paths, and access tokens are absent.
[ ] Operational wet-lab parameters are absent.
[ ] Manual public-safety review is documented before public release.
Assign a decision category: Select the most appropriate decision category and record the reason for the decision.
[ ] Reportable: QC, controls, documentation, and review support release. Recommended action: Proceed through approved local reporting route
[ ] Manual review: Result needs analyst or supervisor review. Recommended action: Hold final wording until review is complete
[ ] Repeat: QC, control, coverage, or documentation issue affects confidence. Recommended action: Repeat or reprocess according to local policy
[ ] Not reportable: Evidence is insufficient, invalid, or unsupported. Recommended action: Do not report; record reason
[ ] Training only: Synthetic or demonstration example. Recommended action: Use for training or portfolio context only
Record expected result and handover notes: Summarize what the completed checklist should allow a qualified reviewer to understand.
[ ] A completed review record should allow another qualified reviewer to understand which samples were included, which controls were reviewed, which workflow version was used, what QC evidence was available, what decision was made, and what caveats or handover notes apply.