Treasure: A Sensitive Pipeline for Species-Level and Functional Microbiome Profiling
Avelar, D. d. S.; Teixeira, E. B.; Casseb, S. M. M.; Moreira, F.; Assumpcao, P. P.
Show 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.
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