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

18. Finding and Characterizing Repeats in Plant Genomes

Jacques Nicolas, Sébastien Tempel, Anna-Sophie Fiston-Lavier, and Emira Cherif

19. Gene Co-Expression Network Analysis

Juan D. Montenegro

20. Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies

Philipp Emanuel Bayer

21. Managing High-Density Genotyping Data with Gigwa

Guilhem Sempéré, Pierre Larmande, and Mathieu Rouard

22. Machine Learning for Image Analysis: Leaf Disease Segmentation

Monica F. Danilevicz and Philipp E. Bayer

23. Analysis of Bisulphite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions

HueyTyng Lee

24. Long Intergenic Non-Coding RNA (lincRNA) Discovery from Non-Strand Specific RNA-Seq Data

Agnieszka Golicz

25. Linkage Disequilibrium Statistics and Block Visualization

Jacob Marsh

26. Analysis of Small RNA Sequencing Data in Plants

Vanika Garg and Rajeev K. Varshney

27. Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases

Parul Gupta, Sushma Naithani, Justin Preece, Sunghwan Kim, Tiejun Cheng, Peter D'Eustachio, Justin Elser, Evan E. Bolton, and Pankaj Jaiswal

28. AgroLD: A Knowledge Graph Database for Plant Functional Genomics

Pierre Larmande, Gildas Tagny Ngompe, Aravind Venkatesan, and Manuel Ruiz