Plant Bioinformatics Methods and Protocols

This new edition focuses on applied bioinformatics with specific applications to crops, model and diverse plant species. The scope extends from the genome to the phenome and includes aspects of data management, analysis, visualization, and integration. The methods and approaches found within reflect the increasing use of high performance computing infrastructure to analyze and manage the enormous volume of data being generated by the latest high throughput technologies, the establishment and further maturation of major database systems and repositories, as well as the introduction of new approaches such as machine learning. Written for the highly successful Methods in Molecular Biology series, the chapters include the kind of detailed implementation advice that leads to successful research results. 

Using GenBank and SRA.- Scripting Analyses of Genomes in Ensembl Plants.- CyVerse for Reproducible Research: RNA-Seq Analysis.- Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources.- Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.- CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource.- The Barley and Wheat Pan-Genomes.- Basics of Bash.- Pipeline Automation via Snakemake.- SciApps: An Automated Platform for Processing and Distribution of Plant Genomics Data.- Trimming and Validation of Illumina Short Reads Using Trimmomatic, Trinity Assembly, and Assessment of RNA-Seq Data.- De Novo Assembly of Linked Reads Using Supernova 2.0.- Applications of Optical Mapping for Plant Genome Assembly and Structural Variation Detection.- Making a Pangenome Using the Iterative Mapping Approach.- Construction of Practical Haplotype Graph (PHG) with the Whole Genome Sequence Data.- Visualization Tools for Genomic Conservation.- Annotation of Protein-Coding Genes in Plant Genomes.- Finding and Characterizing Repeats in Plant Genomes.- Gene Co-Expression Network Analysis.- Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies.- Managing High-Density Genotyping Data with Gigwa.- Machine Learning for Image Analysis: Leaf Disease Segmentation.- Analysis of Bisulphite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions.- Long Intergenic Non-Coding RNA (lincRNA) Discovery from Non-Strand Specific RNA-Seq Data.- Linkage Disequilibrium Statistics and Block Visualization.- Analysis of Small RNA Sequencing Data in Plants.- Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases.- AgroLD: A Knowledge Graph Database for Plant Functional Genomics.