AppliedGenomeResearch

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AppliedGenomeResearch

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course about NGS data processing: genomics and transcriptomics

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# AppliedGenomeResearch
course about NGS data processing: genomics and transcriptomics

Nd-1 sequencing reads for de novo genome assembly and read mapping against Col-0 reference:
[10.4119/unibi/2941047](https://doi.org/10.4119/unibi/2941047)

## References
- NGS assembly of Nd-1 and origin of sequencing reads:  https://doi.org/10.1371/journal.pone.0164321
- Improved annotation: https://doi.org/10.1186/s13104-017-2985-y
- PacBio assembly of Nd-1: https://doi.org/10.1101/407627 
- De novo transcriptome assembly: https://doi.org/10.3389/fmolb.2018.00062
- Integrating Molecular Biology and Bioinformatics Education: https://doi.org/10.1515/jib-2019-0005

## Additional literature
- Pucker B, Irisarri I, de Vries J and Xu B (2022). Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions. Quantitative Plant Biology, 3, E5. doi: [10.1017/qpb.2021.18](https://doi.org/10.1017/qpb.2021.18).
- Pucker, B. (2024). Functional Annotation – How to Tackle the Bottleneck in Plant Genomics. Preprints. doi: [10.20944/preprints202402.0645.v1](https://www.preprints.org/manuscript/202402.0645).
- de Oliveira, J. A. V. S.; Choudhary, N.; Meckoni, S. N.; Nowak, M. S.; Hagedorn, M.; Pucker, B. (2025). Cookbook for Plant Genome Sequences. BMC Genomics (2026). doi: [10.1186/s12864-026-12623-z](https://doi.org/10.1186/s12864-026-12623-z).

## Contact:
[Boas Pucker (University of Bonn)](https://www.izmb.uni-bonn.de/en/pbb/contact)

AppliedGenomeResearch

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