Whole-Genome Annotation with BRAKER

By Katharina Jasmin Hoff, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke. Methods in molecular biology, 2019

573 citations recorded by the source corpus.

BRAKER is a pipeline for highly accurate and fully automated gene prediction in novel eukaryotic genomes. It combines two major tools: GeneMark-ES/ET and AUGUSTUS. GeneMark-ES/ET learns its parameters from a novel genomic sequence in a fully automated fashion; if available, it uses extrinsic evidence for model refinement. From the protein-coding genes predicted by GeneMark-ES/ET we select a set for training AUGUSTUS, one of the most accurate gene finding tools that, in contrast to GeneMark-ES/ET, integrates extrinsic evidence already into the gene prediction step. The first published version, BRAKER1, integrated genomic footprints of unassembled RNA-Seq reads into the training as well as into the prediction steps. The pipeline has since been extended to the integration of data on mapped cross-species proteins, and to the usage of heterogeneous extrinsic evidence, both RNA-Seq and protein alignments. In this book chapter, we briefly summarize the pipeline methodology and describe how to apply BRAKER in environments characterized by various combinations of external evidence.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d07a696ed112c4967da624078a62f055859d2aa6

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Citations in the corpus

A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas (2020, unknown): “5 (BRAKER, RRID:SCR 018964) [62] using only the paired-end RNAseq datasets (see Supplementary Table S3).”
TSEBRA: transcript selector for BRAKER (2021, background): “single-source evidence mode when using RNA-seq and proteins simultaneously [31,32].”