NAM Genomes Save
Detailed bioinformatics scripts and methods used in the NAM genome paper.
NAM-genomes :corn: :corn: :corn:
For co-authors (click to expand)
NAM genome paper related scripts and workflows
Please follow this structure for your contribution.
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Add all the scripts for one specific task inside aptly named folder (eg:
agp-generation), use hyphen for gaps and use all lower-case letters (if possible). -
Add a README.md file within the folder, specifically addressing the order and inputs required for the scripts you put in the folder
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If you have any figures, please create a folder within that section folder (please name it "assets") and drop them there. You can also add other files or things that doesn't qualify as scripts in there.
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Please check if your section is linked correctly from the main README page
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Please let me know if you have any questions or have any suggestions!
Go, NAMsters!
Table of contents:
- Genome assembly methods (contig, hybrid scaffold and pseudomolecule construction )
- Quality control (raw data: Illumina, PacBio, RNA-Seq; and Assembly)
- Gene prediction and annotation (evidence-based, BRAKER, merging annotations)
- Centromere annotation
- Knob analyses
- DNA methylation and Accessible Chromatin Regions (ACR) analyses
- PanGenome analyses
- Transposable Element Annotation
- Tandem Repeat Arrays
- Structural variation detection
- Analysis of Flowering-time Genes
- Analyses of disease resistance Genes
- Population Genetic Analysis (GERP, abc)
- Genome-wide Association Study and Variance Component Analysis
- Fractionation Analysis
Figures/Plots
Figures and plots used in the publication
Links for external data
- CyVerse Data Commons
- MaizeGDB NAM-page, GenomeBrowser, FTP site.
- Gramene
- Raw Datasets (PRJEB31061 and PRJEB32225)
- PacBio
- Illumina
- RNAseq: E-MTAB-8633 and E-MTAB-8628
- BioNano
- Methylation data: E-MTAB-10088
- NLR trees
- NAM-webpage
Citation
Matthew B Hufford, Arun S Seetharam, Margaret R Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A Ricci, Tingting Guo, Andrew Olson, Yinjie Qiu, Rafael Della Coletta, Silas Tittes, Asher I Hudson, Alexandre P. Marand, Sharon Wei, Zhenyuan Lu, Bo Wang, Marcela K Tello-Ruiz, Rebecca D Piri, Na Wang, Dong won Kim, Yibing Zeng, Christine H O’Connor, Xianran Li, Amanda M Gilbert, Erin Baggs, Ksenia V Krasileva, John L Portwood II, Ethalinda KS Cannon, Carson M Andorf, Nancy Manchanda, Samantha J Snodgrass, David E Hufnagel, Qiuhan Jiang, Sarah Pedersen, Michael L Syring, David A Kudrna, Victor Llaca, Kevin Fengler, Robert J. Schmitz, Jeffrey Ross-Ibarra, Jianming Yu, Jonathan I Gent, Candice N Hirsch, Doreen Ware, R Kelly Dawe. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. bioRxiv, 10.1101/2021.01.14.426684, 2021.
Contacts
Please check our contributions page for all the authors who worked on this GitHub documentation (and the sections they worked on!).
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