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Helixer with post-processing via AUGUSTUS

Additional Dependencies

This requires AUGUSTUS and all its dependencies, see: https://github.com/Gaius-Augustus/Augustus

When to use or not

For ab initio prediction of primary gene models helixer + AUGUSTUS does not have quite the same raw accuracy as running helixer + helixer_post_bin (as done when running Helixer.py), on species we've checked so far. If this is your use-case, we recommend using helixer + helixer_post_bin (e.g. via Helixer.py as described in the main README.md); it's also substantially faster.

However, helixer + AUGUSTUS does provide alternative transcripts, which the other does not, and helixer + AUGUSTUS should be extensible for integration with any extrinsic data sources that AUGUSTUS supports.

The process

First, generate Helixer predictions for the genome in question (using the same example data as the main readme).

# this exactly matches the 'example broken into individual steps' from the README.md
fasta2h5.py --species Arabidopsis_lyrata --h5-output-path Arabidopsis_lyrata.h5 --fasta-path Arabidopsis_lyrata.v.1.0.dna.chromosome.8.fa
helixer/prediction/HybridModel.py --load-model-path models/land_plant.h5 --test-data Arabidopsis_lyrata.h5 --overlap --val-test-batch-size 32 -v

Second, convert these predictions into hints

python3 <path_to>/Helixer/scripts/predictions2hints.py -p predictions.h5 -d Arabidopsis_lyrata.h5 -o Arabidopsis_lyrata_helixer_hints.gff3

Third, get extrinsic config setup for Helixer-style hints. Bonus and penalty weighting has not been optimized, and it may be worth it to adjust these. To combine with any other hint sources, the extrinsic cfg file will need to be updated according to AUGUSTUS documentation.

wget https://raw.githubusercontent.com/weberlab-hhu/helixer_scratch/master/method_comp/running_augustus/cgp.extrinsic.cfg

Fourth, run AUGUSTUS

# adjust the following to the best/closest AUGUSTUS species model 
# that you have available for your target species
augustus_sp=arabidopsis
  
# run augustus
augustus --species=$augustus_sp Arabidopsis_lyrata.v.1.0.dna.chromosome.8.fa --softmasking=1 \
    --extrinsicCfgFile=cgp.extrinsic.cfg --hintsfile=Arabidopsis_lyrata_helixer_hints.gff3 \
    --gff3=on --UTR=on > Arabidopsis_lyrata_chromosome8_helixer_augustus.gff3
# depending on genome size, this may take a long time (from several hours to days)