When publishing results of this BRAKER run, please cite the following sources:
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Hoff, K. J., Lange, S., Lomsadze, A., Borodovsky, M., & Stanke, M. (2016). BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics, 32(5), 767-769.

Bruna, T., Hoff, K.J., Lomsadze, A., Stanke, M., & Borodovsky, M. (2021). BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database. NAR Genomics and Bioinformatics 3(1), lqaa108.

Hoff, K. J., Lomsadze, A., Borodovsky, M., & Stanke, M. (2019). Whole-genome annotation with BRAKER. In Gene Prediction (pp. 65-95). Humana, New York, NY.

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., ... & Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078-2079.

Barnett, D. W., Garrison, E. K., Quinlan, A. R., Strömberg, M. P., & Marth, G. T. (2011). BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics, 27(12), 1691-1692.

Lomsadze, A., Burns, P. D., & Borodovsky, M. (2014). Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm. Nucleic acids research, 42(15), e119-e119.

Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12(1), 59.

Stanke, M., Diekhans, M., Baertsch, R., & Haussler, D. (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, 24(5), 637-644.

Stanke, M., Schöffmann, O., Morgenstern, B., & Waack, S. (2006). Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics, 7(1), 62.