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Contents

Preface .. . . . . . . . . . . . . . . . . . . . v
Contributors.. . . . . . . . . . . . . . . . xi
1 Using GenBank and SRA . . . . .  . . . . . . . 1
2 Scripting Analyses of Genomes in Ensembl Plants. . . . . .  . . . . . . 27
3 CyVerse for Reproducible Research: RNA-Seq Analysis . . . . . . . . . . . . . 57
4 Doing Genetic and Genomic Biology Using the Legume
Information System and Associated Resources. . . . . . . . .  . . . . . 81
5 Gramene: A Resource for Comparative Analysis of Plants Genomes
and Pathways .. . . . . . . . . . 101
6 CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource . . . . . . . . . . . 133
7 The Barley and Wheat Pan-Genomes . . . . . . . . . . . 147
8 Basics of Bash .. . . . . . . . . 161
9 Pipeline Automation via Snakemake . . . . . . . . . . . . 181
10 SciApps: An Automated Platform for Processing and Distribution
of Plant Genomics Data .....197
11 Trimming and Validation of Illumina Short Reads Using Trimmomatic,
Trinity Assembly, and Assessment of RNA-Seq Data . . . . . . . . . .  . . . . . 211
12 De Novo Assembly of Linked Reads Using Supernova 2.0 . . . . . . . . . . . . . 233
13 Applications of Optical Mapping for Plant Genome Assembly
and Structural Variation Detection . . . . . .  . . . 245
14 Making a Pangenome Using the Iterative Mapping Approach . . . . . . . . . 259
15 Construction of Practical Haplotype Graph (PHG)
with the Whole-Genome Sequence Data. . . . . . . . . . 273
16 Visualization Tools for Genomic Conservation . . . . . . . . . . . . 285
17 Annotation of Protein-Coding Genes in Plant Genomes. . . . . . . . . . . . . 309
18 Finding and Characterizing Repeats in Plant Genomes . . . . . . . . . .. . . . . . 327
19 Gene Co-expression Network Analysis. . . . . . . . . . . . 387
20 Skim-Based Genotyping by Sequencing Using a Double Haploid
Population to Call SNPs, Infer Gene Conversions, and Improve
Genome Assemblies .. . . . 405
21 Managing High-Density Genotyping Data with Gigwa . . . . . . . . .  . . . . . . 415
22 Machine Learning for Image Analysis: Leaf Disease Segmentation . . . . . . . . . . . . 429
23 Analysis of Bisulfite Sequencing Data Using Bismark
and DMRcaller to Identify Differentially Methylated Regions . . . . . . . . . . . . . . . . 451
24 Long Intergenic Noncoding RNA (lincRNA) Discovery
from Non-Strand-Specific RNA-Seq Data. . . . . . .. . . . . . . 465
25 Linkage Disequilibrium Statistics and Block Visualization. . . . .. . . . . 483
26 Analysis of Small RNA Sequencing Data in Plants. . . . . .  . . . . . . . 497
27 Plant Reactome and PubChem: The Plant Pathway
and (Bio)Chemical Entity Knowledgebases . . . . . . . . .. . . . . 511
28 AgroLD: A Knowledge Graph Database for Plant Functional
Genomics .. . . . . . . . . . . . . 527
Index .. . . . . .. . . 541

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