Treasure: A Sensitive Pipeline for Species-Level and Functional Microbiome Profiling

Abstract

Next Generation Sequencing (NGS) methods, such as 16S rRNA amplicon sequencing and Whole Genome Sequencing (WGS), enable taxonomic analyses but have limitations. This project proposes the development of a computational tool capable of performing functional analysis of the most abundant microorganisms within a microbiome based on taxonomic analysis. The proposed method integrates the tools Kraken, Gffread, and Salmon. Compared to Samsa 2, a commonly used pipeline for RNA-Seq Total samples, the new approach demonstrated superior performance across all evaluated scenarios (p < 0.01). The tool aims to functionally characterize the microbiome of regions affected by Gastric Cancer (GC) and adjacent areas, assess associations between survival, expression/abundance, and identify potential microbial biomarkers for GC.