| Required software | Version |
|---|---|
| BRAKER | v2.1.2 |
| AUGUSTUS | v3.3.3 |
| HISAT | v2.1.0 |
| StringTie | v2.1.4 |
| TransDecoder | v5.5.0 |
| GffCompare | v0.11.2 |
| GffRead | v0.12.1 |
| SeqKit | v2.0 |
#Chips to run BRAKER
- Gaius-Augustus/BRAKER#126
- https://github.com/Gaius-Augustus/Augustus/commit/49978fa94ff197cd3dea82cce01c443c95a48b55#diff-e7897247d4f0d137d6312761aeec94d2
- https://github.com/Gaius-Augustus/Augustus/commit/3da1d64553bafb7d0a80decea0b09e11dfd4a872
This method was used in paper below.
Yoshioka Y, Suzuki G, Zayasu Y, Yamashita H, and Shinzato C (2022) Comparative genomics highlight the importance of lineage-specific gene families in evolutionary divergence of the coral genus, Montipora. BMC Ecology and Evolution. 22:71. Link
Gene models are available at OIST Marine Genomics Unit Genome Browser