Bioinformatics Methods in Modern Malaria Research: Tools, Pipelines, and Gaps in Application

This review evaluates bioinformatics methods central to modern malaria research, comparing key tools, pipelines, and integrated platforms such as Malaria-Profiler and MalariaGEN. It examines mature workflows for whole-genome sequencing, amplicon, and RNA-seq data processing spanning quality control, alignment, and variant calling and their applications in drug resistance surveillance, transmission network analysis, and field diagnostics. The review also identifies persistent gaps in application, including reference genome bias, host DNA contamination, and infrastructure and skills deficits in malaria-endemic regions, arguing that bioinformatics must shift from a research luxury to a standard public health tool through regional training and sovereign computational infrastructure.