Life Sciences NGS Analysis
ChatGPT pluginGuided NGS routing and local execution for sequencing analysis
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A guided intake, routing, and execution plugin for next-generation sequencing workflows. It helps Codex inspect local sequencing inputs, ask only the missing assay-specific questions, choose public or freely accessible runtime-installable packages where possible, check existing tool availability before any install, and execute supported local workflows with validation, logs, manifests, QC reports, and artifact indexes. It includes deeper decision skills for BCL demultiplexing, FASTQ QC execution and interpretation, germline, somatic and UMI-panel DNA variants, bulk RNA-seq count generation and differential expression, ATAC-seq, ChIP-seq/CUT&RUN/CUT&Tag, and embedded post-count scRNA-seq QC.
Example prompts
- “Guide me through the minimum required NGS analysis questions, inspect available BCL/FASTQ files or count matrices, choose the right public pipeline or deeper assay-specific skill, check whether required tools already exist, and execute supported local workflows with pre-execution validation and artifact capture.”
Skills
ngs-amplicon-microbiome
Kick off public 16S, 18S, ITS, COI, or other marker-gene amplicon microbiome workflows using nf-core/ampliseq, QIIME2, DADA2, and Cutadapt.
ngs-analysis-router
Route BCL, FASTQ, BAM/CRAM, count-matrix, or VCF sequencing requests to the right public NGS analysis skill and ask only the missing assay-specific setup questions.
ngs-atacseq-peaks-qc
Run or plan ATAC-seq QC, alignment, TSS enrichment, fragment-size, blacklist, peak-calling, consensus peak, and differential accessibility workflows.
ngs-bcl-to-fastq
Validate Illumina BCL run folders and sample sheets, plan demultiplexing, review index/UMI/lane choices, run BCL-to-FASTQ conversion, and interpret demux metrics while surfacing license/download boundaries.
ngs-bulk-rnaseq
Dispatch bulk RNA-seq requests to FASTQ-to-count QC or count-matrix differential-expression skills using nf-core/rnaseq, STAR, Salmon, featureCounts, MultiQC, and R/Bioconductor workflows.
ngs-bulk-rnaseq-counts-qc
Run or plan bulk RNA-seq FASTQ-to-count processing with sample-sheet, strandedness, genome annotation, alignment or pseudoalignment, MultiQC, and count-matrix QC checks.
ngs-bulk-rnaseq-differential-expression
Run or plan bulk RNA-seq differential-expression analysis from count matrices with replicate, design formula, contrast, batch, normalization, QC plot, and result-table checks.
ngs-chip-cutrun-peaks-qc
Run or plan ChIP-seq, CUT&RUN, or CUT&Tag QC, control handling, spike-in, peak calling, broad-vs-narrow target selection, replicate, bigWig, and differential binding workflows.
ngs-dna-germline-variants
Run or plan deep germline WGS, WES, targeted-panel, cohort, or trio variant-calling workflows with reference-build, known-sites, QC, joint-calling, and annotation checks.
ngs-dna-somatic-variants
Run or plan tumor-normal, tumor-only, WGS, WES, or cancer-panel somatic variant workflows with pairing, contamination, panel-of-normals, purity, QC, and annotation checks.
ngs-dna-umi-panel-variants
Run or plan targeted DNA panel variant workflows that use UMIs, duplex consensus reads, molecular barcodes, low-frequency calling, target coverage, and panel-specific QC.
ngs-dna-variant-calling
Dispatch WGS, WES, or targeted DNA variant requests to germline, somatic, or UMI-panel skills, then plan public nf-core/sarek, GATK4, DeepVariant, samtools, or bcftools workflows.
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ngs-epigenomics-peaks
Dispatch ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag requests to assay-specific QC, alignment, signal-track, peak-calling, consensus, and differential peak workflows.
ngs-fastq-qc
Validate FASTQ inputs, run local FastQC/MultiQC QC, interpret QC signals, and optionally execute fastp or Cutadapt trimming branches without overwriting raw reads.
ngs-runtime-env
Check whether public NGS tools and packages already exist before downloading, installing, or running a sequencing pipeline.
ngs-scrna-seq
Route single-cell or single-nucleus RNA-seq FASTQs to public count-generation workflows and defer post-count matrix QC, annotation, clustering, and UMAP analysis to the embedded scrna-seq-qc skill.
ngs-shotgun-metagenomics
Kick off public shotgun metagenomics QC, host-depletion, taxonomic profiling, and functional profiling workflows using nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN.
scrna-seq-qc
Process, quality-control, annotate, and visualize single-cell or single-nucleus RNA-seq datasets across tissues and species. Use when Codex needs to build, adapt, or review a general scRNA-seq QC pipeline; choose dataset-appropriate cell-level filters from QC distributions; run required scDblFinder-based doublet and ambient-RNA filtering; annotate cells with matched references or marker-based fallbacks; or generate global and per-group UMAP visualizations for large scRNA-seq datasets.
- Categories
- Sign-in
- On Install
- Capabilities
- Interactive, Read, Write
- Availability
- Available
- Version
- 1.0.3
- Created
- June 3, 2026
- More info