Lieutenant Harry Braker
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It enables the usage of RNA-seq and protein data in a fully automated pipeline to train and predict highly reliable genes with GeneMark-ETP and AUGUSTUS. The result of the pipeline is the combined gene set of both gene prediction tools, which only contains genes with very high support from extrinsic evidence.
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes - Gaius-Augustus/BRAKER
BRAKER3 enables the usage of RNA-seq and protein data in a fully automated pipeline to train and predict highly reliable genes with GeneMark-ETP and AUGUSTUS. The result of the pipeline is the combined gene set of both gene prediction tools, which only contains genes with very high support from extrinsic evidence.
In contrast to other genome annotation pipelines, such as e.g. MAKER [ 11, 12 ], BRAKER trains both gene finders in a fully automated fashion before applying them to the genome. For gene prediction, both GeneMark-ES/ET and AUGUSTUS use statistical models with a large number of parameters.
- Katharina J Hoff, Alexandre Lomsadze, Mark Borodovsky, Mark Borodovsky, Mario Stanke
- 10.1007/978-1-4939-9173-0_5
- 2019
- 2019
Jun 10, 2023 · These many advancements and the steady increase in popularity of the previous BRAKER tools motivated us to develop a new version of the BRAKER pipeline that can utilize both transcript and protein homology extrinsic evidence by incorporating GeneMark-ETP, AUGUSTUS, and TSEBRA into a novel workflow.
- 10.1101/2023.06.10.544449
- 2023 Jun
braker is a tool that uses RNA-seq and protein data to train and predict protein coding genes with GeneMark-ETP and AUGUSTUS. It is part of the BRAKER suite of tools for novel eukaryotic genomes.
You have to install the 'long_reads' branch of BRAKER via GitHub https://github.com/Gaius-Augustus/BRAKER. ⚠️ The long read protocol does not work with e.g. an Anaconda installation of BRAKER because the long read branch is not part of the BRAKER release, yet. Clone BRAKER:
