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Book chapter - Peer-reviewed, 2022

Computational analysis of HTS data and its application in plant pathology.

Piombo, Edoardo; Dubey, Mukesh

Abstract

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

High-throughput sequencing; Genome assembly; Functional annotation; Transcriptomics; Differential expression; Metabarcoding; Small RNA; miRNA; Target prediction

Published in

Methods in Molecular Biology
2022, number: 2536, pages: 275-307
Book title: Plant Pathology : Method and Protocols
ISBN: 978-1-0716-2516-3, eISBN: 978-1-0716-2517-0
Publisher: Springer