| name | ngs-analysis |
| description | Practical next-generation sequencing analysis support for bulk RNA-seq, variant calling, alignment, preprocessing, and workflow assembly. Use when working from FASTQ or BAM/VCF inputs, setting up QC, choosing aligners or quantifiers, organizing reproducible NGS pipelines, or preparing downstream differential or variant analyses. |
NGS Analysis
Run NGS tasks with explicit sample tracking, reproducible commands, and pipeline choices that match the assay.
Workflow
- Identify assay, read structure, reference assets, and expected endpoint before running tools.
- Check file integrity, sample sheet consistency, lane structure, and naming conventions first.
- Run QC before major processing and keep pre-filter and post-filter metrics.
- Choose assay-specific tooling rather than forcing one generic pipeline across RNA-seq, DNA-seq, and single-cell data.
- Preserve provenance for every intermediate: command, version, reference, and parameter changes.
- Summarize outputs in terms a collaborator can act on: pass-fail QC, counts, variant sets, DE tables, or missing inputs.
Guardrails
- Never mix genome builds or annotation releases silently.
- Keep tumor-normal pairing, replicate structure, and strandedness explicit.
- Treat aligner defaults as starting points, not biological truth.
- Separate workflow failures from biologic negatives.
References
- Read
references/pipeline-selection.md to choose the right NGS path.
