Guided NGS routing and local execution for sequencing analysis
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. More
What you can ask 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. Copy
· NGS Router skill
Skills 18 in the ChatGPT listing
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 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. ATAC-seq Peaks QC Run or plan ATAC-seq QC, alignment, TSS enrichment, fragment-size, blacklist, peak-calling, consensus peak, and differential accessibility workflows. 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. Bulk RNA-seq 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. Bulk RNA-seq Counts 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. Bulk RNA-seq DE 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. ChIP/CUT&RUN 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. Germline DNA 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. Somatic DNA 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. 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. DNA Variants 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. 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. 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 Check whether public NGS tools and packages already exist before downloading, installing, or running a sequencing pipeline. Single-cell RNA-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. 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. 
Inductive Bio#285