SeqMate: A Novel Large Language Model Pipeline for Automating RNA Sequencing
Devam Mondal, Atharva Inamdar
TL;DR
RNA-seq analysis is hindered by complex toolchains and usability barriers for non-experts. SeqMate proposes an LLM-driven autonomous pipeline that orchestrates data preparation, analysis, and reporting starting from raw FASTQ data, using LangChain and external bioinformatics tools to perform steps from trimming and alignment to differential expression and literature-backed reporting. The approach contributes a configurable, end-to-end, one-click workflow that adapts to specific use cases and generates narrative insights with citations, while transparently addressing limitations such as hallucinations and privacy concerns. This work has practical impact by democratizing RNA-seq analytics and signaling a path toward expanding LLM-assisted bioinformatics pipelines for broader applications.
Abstract
RNA sequencing techniques, like bulk RNA-seq and Single Cell (sc) RNA-seq, are critical tools for the biologist looking to analyze the genetic activity/transcriptome of a tissue or cell during an experimental procedure. Platforms like Illumina's next-generation sequencing (NGS) are used to produce the raw data for this experimental procedure. This raw FASTQ data must then be prepared via a complex series of data manipulations by bioinformaticians. This process currently takes place on an unwieldy textual user interface like a terminal/command line that requires the user to install and import multiple program packages, preventing the untrained biologist from initiating data analysis. Open-source platforms like Galaxy have produced a more user-friendly pipeline, yet the visual interface remains cluttered and highly technical, remaining uninviting for the natural scientist. To address this, SeqMate is a user-friendly tool that allows for one-click analytics by utilizing the power of a large language model (LLM) to automate both data preparation and analysis (differential expression, trajectory analysis, etc). Furthermore, by utilizing the power of generative AI, SeqMate is also capable of analyzing such findings and producing written reports of upregulated/downregulated/user-prompted genes with sources cited from known repositories like PubMed, PDB, and Uniprot.