# Katharina J. Hoff
# November 25th 2020
# Species specific AUGUSTUS parameters for Phaeodactylum tricornutum

Augustus parameter set name: Phaeodactylum_tricornutum

Lineage: Eukaryota; Sar; Stramenopiles; Ochrophyta; Bacillariophyta; Bacillariophyceae; Bacillariophycidae; Naviculales; Phaeodactylaceae; Phaeodactylum

This parameter set was created with BRAKER on the basis of genome assembly https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/150/955/GCF_000150955.2_ASM15095v2/GCF_000150955.2_ASM15095v2_genomic.fna.gz and OrthoDb proteins https://v100.orthodb.org/download/odb10_plants_fasta.tar.gz

Call:

braker.pl --genome=genome.fa --prot_seq=proteins.fasta --softmasking --cores=8 --species=Phaeodactylum_tricornutum --epmode

Flanking region size: 802
Number of generated training genes: 1364 nonredundant genes, 300 set aside for testing, 300 set aside for optimize_augustus.pl time consuming steps

Initial accuracy on test set: 0.8322
Accuracy on test set after optimize_augustus.pl: 0.854333333333333

With this parameter set, BRAKER predicted 11503 genes (Augustus with hints in the target genome). For comparison, the RefSeq annotation contains 10408 genes.

This parameter set was generated in a fully automated fashion for supporing the POMPU project (http://www.pompu-project.de/).

If using this parameter set, please cite:

Bruna, T., Hoff, K., Stanke, M., Lomsadze, A., & Borodovsky, M. (2020). BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database. bioRxiv. https://www.biorxiv.org/content/10.1101/2020.08.10.245134v1.abstract