1. Using GenBank and SRA
Eric W. Sayers, Chris O'Sullivan, and Ilene Karsch-Mizrachi
2. Scripting Analyses of Genomes in Ensembl Plants
Bruno Contreras-Moreira, Guy Naamati, Marc Rosello, James E. Allen, Sarah E. Hunt, Matthieu Muffato, Astrid Gall, and Paul Flicek
3. CyVerse for Reproducible Research: RNA-Seq Analysis
Jason Williams
4. Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources
Sven Redsun, Sam Hokin, Connor T. Cameron, Alan M. Cleary, Joel Berendzen, Sudhansu Dash, Anne V. Brown, Andrew Wilkey, Jacqueline D. Campbell, Wei Huang, Scott R. Kalberer, Nathan T. Weeks, Steven B. Cannon, and Andrew D. Farmer
5. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways
Marcela Karey Tello-Ruiz, Pankaj Jaiswal, and Doreen Ware
6. CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource
Mark Winfield, Paul Wilkinson, Amanda Burridge, Alexandra Allen, Jane Coghill, Christy Waterfall, Keith Edwards, and Gary Barker
7. The Barley and Wheat Pan-Genomes
Nadia Kamal, Thomas Lux, Murukarthick Jayakodi, Georg Haberer, Heidrun Gundlach, Klaus F.X. Mayer, Martin Mascher, and Manuel Spannagl
8. Basics of Bash
Robyn Anderson
9. Pipeline Automation via Snakemake
Jakob Petereit
10. SciApps: An Automated Platform for Processing and Distribution of Plant Genomics Data
Liya Wang, Zhenyuan Lu, Peter Van Buren, and Doreen Ware
11. Trimming and Validation of Illumina Short Reads Using Trimmomatic, Trinity Assembly, and Assessment of RNA-Seq Data
Steven O. Sewe, Gonçalo Silva, Paulo Sicat, Susan E. Seal, and Paul Visendi
12. De Novo Assembly of Linked Reads Using Supernova 2.0
Paul Visendi
13. Applications of Optical Mapping for Plant Genome Assembly and Structural Variation Detection
Yuxuan Yuan
14. Making a Pangenome Using the Iterative Mapping Approach
Cassandria Tay Fernandez
15. Construction of Practical Haplotype Graph (PHG) with the Whole Genome Sequence Data
Pradeep Ruperao, Prasad Gandham, and Abhishek Rathore
16. Visualization Tools for Genomic Conservation
Venkat Bandi, Carl Gutwin, Jorge Núñez Siri, Eric Neufeld, Andrew Sharpe, and Isobel Parkin
17. Annotation of Protein-Coding Genes in Plant Genomes
Bhavna Hurgobin
