High-throughput sequencing is a basic tool of biological research, and it is extensively used in plant pathology projects. Here, we describe how to handle data coming from a variety of sequencing experiments, focusing on the analysis of Illumina reads. We describe how to perform genome assembly and annotation with DNA reads, correctly analyze RNA-seq data to discover differentially expressed genes, handle amplicon sequencing data from microbial communities, and utilize small RNA sequencing data to predict miRNA sequences and their putative targets.
Keywords: Differential expression; Functional annotation; Genome assembly; High-throughput sequencing; Metabarcoding; Small RNA; Target prediction; Transcriptomics; miRNA.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.