Life Sciences NGS Analysis

Life Sciences NGS Analysis Plugin

This plugin provides a guided intake and execution layer for common next-generation sequencing analyses. It routes users from BCL or FASTQ files to public, reproducible pipelines while checking local tool availability before installing anything.

What It Does

• Inspects sequencing inputs before asking questions.
• Asks the minimum assay-specific questions needed to choose an analysis route.
• Prefers public, runtime-installable tools and nf-core workflows where practical.
• Runs tool preflight checks before suggesting downloads or installs.
• Keeps proprietary, credentialed, or cloud-upload paths explicit instead of silently using them.
• Treats preflight as validation before executing approved local workflows where supported.
• Produces timestamped run directories with manifests, validation summaries, logs, QC reports, exact command timing/return-code detail, checksummed artifact indexes, and input-to-output lineage tables.
• Produces native visualization bundles under visualizations/ when a lane has enough downstream data to plot.

Included Skills

• ngs-analysis-router: top-level intake and routing.
• ngs-runtime-env: package/tool existence checks and install planning.
• ngs-bcl-to-fastq: BCL run-folder validation, demultiplexing, and demux metric review.
• ngs-fastq-qc: FASTQ quality control, trimming decisions, and MultiQC interpretation.
• ngs-dna-variant-calling: WGS/WES/panel variant dispatcher.
• ngs-dna-germline-variants: germline WGS/WES/panel variant calling and QC.
• ngs-dna-somatic-variants: tumor-normal and tumor-only somatic variant calling and QC.
• ngs-dna-umi-panel-variants: UMI, duplex, and low-frequency targeted panel workflows.
• ngs-bulk-rnaseq: bulk RNA-seq dispatcher.
• ngs-bulk-rnaseq-counts-qc: bulk RNA-seq FASTQ-to-count processing and QC.
• ngs-bulk-rnaseq-differential-expression: bulk RNA-seq count-matrix differential expression.
• ngs-scrna-seq: single-cell or single-nucleus RNA-seq FASTQ-to-count kickoff.
• scrna-seq-qc: embedded post-count single-cell QC, annotation, clustering, and UMAP guidance.
• ngs-epigenomics-peaks: ATAC-seq, ChIP-seq, CUT&RUN, and CUT&Tag dispatcher.
• ngs-atacseq-peaks-qc: ATAC-seq QC, peak, consensus, and differential accessibility workflows.
• ngs-chip-cutrun-peaks-qc: ChIP-seq, CUT&RUN, and CUT&Tag QC, control, peak, and differential binding workflows.
• ngs-amplicon-microbiome: 16S/18S/ITS/COI amplicon analysis kickoff.
• ngs-shotgun-metagenomics: shotgun metagenomics taxonomic and functional profiling kickoff.