# Katharina J. Hoff
# August 25th 2021
# Species specific AUGUSTUS parameters for Physcomitrium patens

Augustus parameter set name: Physcomitrium_patens

Lineage: Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Bryophyta; Bryophytina; Bryopsida; Funariidae; Funariales; Funariaceae; Physcomitrium

This parameter set was created with BRAKER on the basis of genome assembly https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/425/GCF_000002425.4_Phypa_V3/GCF_000002425.4_Phypa_V3_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=Physcomitrium_patens --epmode

Flanking region size: 1183
Number of generated training genes: 7246 nonredundant genes, 200 set aside for testing, 200 set aside for optimize_augustus.pl time consuming steps

Initial accuracy on test set: 0.844733333333333
Accuracy on test set after optimize_augustus.pl: 0.840933333333333

With this parameter set, BRAKER predicted 36258 transcripts (Augustus with hints in the target genome). For comparison, the RefSeq annotation contains 48022 transcripts.

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.J., Stanke, M., Lomsadze, A., & Borodovsky, M. (2021). BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database. NAR genomics and bioinformatics, lqaa108.