SeqMate: A Novel Large Language Model Pipeline for Automating RNA Sequencing

TL;DR

SeqMate is an innovative AI-powered pipeline that simplifies RNA sequencing data analysis for biologists by enabling one-click automation and generating comprehensive reports with source citations.

Contribution

It introduces a user-friendly LLM-based platform that automates complex RNA-seq data processing and analysis, making it accessible to non-experts.

Findings

Automates RNA-seq data preparation and analysis with a single click

Generates detailed reports citing sources from biomedical repositories

Reduces technical barriers for biologists in data analysis

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.