ngs-analysis Codex Plugin
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ngs-analysis is a Codex plugin from OpenAI that guides users through next-generation sequencing analysis, starting from BCL or FASTQ intake and routing to either a public pipeline or a supported local workflow. According to its README, it includes separate skills for BCL demultiplexing, FASTQ quality control, DNA variant calling (germline, somatic, and UMI panel), bulk RNA-seq quantification and differential expression, single-cell RNA-seq, epigenomics assays such as ATAC-seq and ChIP-seq, amplicon microbiome profiling, and shotgun metagenomics. Before any installation, it checks for existing local tools and prefers public, freely available packages such as nf-core, FastQC, Salmon, and GATK. Successful local runs produce a timestamped output folder containing validation records, logs, manifests, QC summaries, and checksummed artifact indexes. Per plugin.json, it is released under the MIT license and listed under the Education & Research category.
What you can do with ngs-analysis
- Get guided, assay-specific questions that route you to the right NGS analysis path based on your BCL, FASTQ, or matrix inputs
- Run local execution lanes for FASTQ QC, bulk RNA-seq counting and differential expression, single-cell processing, and DNA variant calling
- Check whether required bioinformatics tools already exist locally and generate a reviewable install plan before anything is installed
- Hand off full workflows to public nf-core pipelines such as sarek, rnaseq, scrnaseq, atacseq, chipseq, ampliseq, and taxprofiler
- Track reference genome and database readiness with dedicated commands (list, check, plan, lock, verify-lock)
- Review completed runs through generated manifests, logs, QC reports, and visualization bundles