Computational analysis of HTS data and its application in plant pathology

Sammanfattning

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.

Nyckelord

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

Publicerad i

Methods in Molecular Biology
2022, nummer: 2536, sidor: 275-307
Titel: Plant Pathology : Method and Protocols
Utgivare: Springer

SLU författare

• Piombo, Edoardo

  • Institutionen för skoglig mykologi och växtpatologi, Sveriges lantbruksuniversitet
    

• Dubey, Mukesh

  • Institutionen för skoglig mykologi och växtpatologi, Sveriges lantbruksuniversitet
    

Associerade SLU-program

SLU Nätverk växtskydd

UKÄ forskningsämne

Genetik
Bioinformatik och systembiologi

Publikationens identifierare

• DOI: https://doi.org/10.1007/978-1-0716-2517-0_17
• ISBN: 978-1-0716-2516-3
• eISBN: 978-1-0716-2517-0

Permanent länk till denna sida (URI)

https://res.slu.se/id/publ/120137