Tools used

1. Pathway annotation for rice and other plants
http://www.gabipd.de/projects/MapMan/

2. Trimmomatic for NGS reads quality control
http://www.usadellab.org/cms/?page=trimmomatic

3. Kraken fro taxonomy classification
http://ccb.jhu.edu/software/kraken/MANUAL.html

4. Bracken for taxonomy estimation using kraken
https://github.com/jenniferlu717/Bracken

5. DESeq2 for differential expression analysis
https://www.huber.embl.de/users/klaus/Teaching/DESeq2-Analysis.pdf

6.Galaxy for multiple analysis (DEGs, FASTQC)
https://usegalaxy.org/

7. The agriGO is a web-based tool and database for the gene ontology analysis. It supports specicial focus on agricultural species and is user-friendly.
http://bioinfo.cau.edu.cn/agriGO/index.php

8. DEBrowser for Differential expression analysis and heat maps viewer
https://debrowser.readthedocs.io/en/master/deseq/deseq.html

9. Web tool allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps.
https://biit.cs.ut.ee/clustvis/

10. A comprehensive database of functionally characterized rice genes 
https://funricegenes.github.io/

11. Mapman - MAPMAN is a user-driven tool that displays large data sets onto diagrams of metabolic pathways or other processes
https://mapman.gabipd.org/

12.REViGO can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms.
The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, or tag clouds. 
http://revigo.irb.hr/

13. Venn diagram
http://jvenn.toulouse.inra.fr/app/index.html
http://bioinformatics.psb.ugent.be/webtools/Venn/