title: BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.
abstract: Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervised training and subsequently generates ab initio gene predictions. AUGUSTUS is a gene finder that usually requires supervised training and uses information from RNA-Seq reads in the prediction step. Complementary strengths of GeneMark-ET and AUGUSTUS provided motivation for designing a new combined tool for automatic gene prediction.
  
  
  
  We present BRAKER1, a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS. As input, BRAKER1 requires a genome assembly file and a file in bam-format with spliced alignments of RNA-Seq reads to the genome. First, GeneMark-ET performs iterative training and generates initial gene structures. Second, AUGUSTUS uses predicted genes for training and then integrates RNA-Seq read information into final gene predictions. In our experiments, we observed that BRAKER1 was more accurate than MAKER2 when it is using RNA-Seq as sole source for training and prediction. BRAKER1 does not require pre-trained parameters or a separate expert-prepared training step.
  
  
  
  BRAKER1 is available for download at http://bioinf.uni-greifswald.de/bioinf/braker/ and http://exon.gatech.edu/GeneMark/
  
  
  
  katharina.hoff@uni-greifswald.de or borodovsky@gatech.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Ernst Moritz Arndt Universität Greifswald, Institute for Mathematics and Computer Science, 17487 Greifswald, Germany.
authors.forename: Katharina J
authors.initials: KJ
authors.lastname: Hoff
authors.affiliation: Ernst Moritz Arndt Universität Greifswald, Institute for Mathematics and Computer Science, 17487 Greifswald, Germany.
authors.forename: Simone
authors.initials: S
authors.lastname: Lange
authors.affiliation: Joint Georgia Tech and Emory University Wallace H Coulter Department of Biomedical Engineering, Atlanta, GA 30332, USA and.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Lomsadze
authors.affiliation: School of Computational Science and Engineering, Atlanta, GA 30332, USA, Joint Georgia Tech and Emory University Wallace H Coulter Department of Biomedical Engineering, Atlanta, GA 30332, USA and Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.
authors.forename: Mark
authors.initials: M
authors.lastname: Borodovsky
authors.affiliation: Ernst Moritz Arndt Universität Greifswald, Institute for Mathematics and Computer Science, 17487 Greifswald, Germany.
authors.forename: Mario
authors.initials: M
authors.lastname: Stanke
mesh_terms: D056890:Eukaryota; D016678:Genome; D012313:RNA; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012313:RNA