Life Sciences NGS Analysis
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. 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.
Install
- 1Add it in ChatGPT
Open Plugins in the ChatGPT sidebar (web or desktop), search for “Life Sciences NGS Analysis” and select +. You'll be asked to sign in to any connected service on first use. Then type @ in a chat to call it.
Skills 15
- Amplicon Microbiome
Plan 16S/ITS/amplicon microbiome analysis
- NGS Router
Route sequencing inputs to the right public analysis workflow
- ATAC-seq Peaks QC
Deep ATAC-seq QC, peak, and accessibility planning
- BCL to FASTQ
Validate BCL run folders and plan FASTQ conversion
- Bulk RNA-seq
Plan bulk RNA-seq counts and DE analysis
- Bulk RNA-seq Counts
Deep FASTQ-to-count processing and QC for bulk RNA-seq
- Bulk RNA-seq DE
Deep differential-expression design and result planning
- ChIP/CUT&RUN Peaks QC
Deep ChIP-seq, CUT&RUN, and CUT&Tag peak workflow planning
- Germline DNA Variants
Deep germline WGS/WES/panel variant workflow planning
- Somatic DNA Variants
Deep tumor-normal or tumor-only somatic variant workflow planning
- UMI Panel Variants
Deep targeted panel and UMI-aware variant workflow planning
- DNA Variants
Plan WGS/WES/panel variant calling
- Epigenomics Peaks
Plan ATAC/ChIP/CUT&RUN/CUT&Tag analysis
- FASTQ QC
Run public FASTQ QC and trimming workflows
- NGS Runtime
Check sequencing packages before installing
Things to 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.”