[meta]
name = "augustus"
category = "annotation"
description = "Gene prediction for eukaryotic genomes using Hidden Markov Models with training support"
tags = ["annotation", "gene-prediction", "eukaryote", "hmm", "genome", "gff"]
author = "oxo-call built-in"
source_url = "https://bioinf.uni-greifswald.de/augustus/"

[context]
concepts = [
    "AUGUSTUS predicts eukaryotic genes using species-specific trained HMM parameters.",
    "Use --species to specify a pre-trained species model (e.g., human, arabidopsis, zebrafish, fly).",
    "List available species with 'augustus --species=help'.",
    "Use --gff3=on for GFF3 output (default is AUGUSTUS-specific format); --outfile for output file.",
    "Evidence integration: use --hintsfile with extrinsic hints (RNA-seq, protein) for better accuracy.",
    "For training on a new species, use the AUGUSTUS training pipeline (autoAug.pl or BRAKER).",
    "AUGUSTUS handles multi-gene prediction across entire chromosomes/scaffolds.",
    "BRAKER (BRAKER1/2/3) automates AUGUSTUS training with RNA-seq or protein evidence.",
]

pitfalls = [
    "Using the wrong species model severely reduces accuracy — choose the closest related organism.",
    "AUGUSTUS without RNA-seq hints may miss many genes in organisms with complex gene structures.",
    "The GFF3 output requires --gff3=on — default AUGUSTUS format is not standard GFF3.",
    "For large genomes, split into chromosomes/scaffolds and run in parallel.",
    "AUGUSTUS is sensitive to repeat-masked input — run RepeatMasker before AUGUSTUS for best results.",
    "Training AUGUSTUS from scratch requires ~1000 manually curated gene structures.",
]

[[examples]]
task = "predict genes in a eukaryotic genome using human parameters"
args = "--species=human genome.fasta --gff3=on > augustus_predictions.gff3"
explanation = "--species=human trained model; --gff3=on standard output format; output redirected to GFF3 file"

[[examples]]
task = "predict genes with RNA-seq hints for improved accuracy"
args = "--species=arabidopsis --hintsfile=rnaseq_hints.gff --extrinsicCfgFile=extrinsic.cfg genome.fasta --gff3=on > improved_predictions.gff3"
explanation = "--hintsfile provides RNA-seq intron/exon hints; --extrinsicCfgFile sets weights for hint integration"

[[examples]]
task = "predict genes and output protein sequences"
args = "--species=fly --gff3=on --protein=on --codingseq=on genome.fasta > fly_predictions.gff3"
explanation = "--protein=on outputs protein sequences in GFF3; --codingseq=on outputs CDS sequences"

[[examples]]
task = "run Augustus on a repeat-masked genome"
args = "--species=zebrafish zebrafish_masked.fasta --gff3=on --softmasking=1 > zebrafish_genes.gff3"
explanation = "--softmasking=1 uses softmasked repeat regions (lowercase) to avoid predicting genes in repeats"
