AUGUSTUS(1)

💖 AUGUSTUS — a gene prediction tool 💖

okay bestie, sit DOWN, because this is the manual page for AUGUSTUS(1) and she is that girl. it's a gene prediction tool, and by the end of this you're gonna be predicting genes like it's nothing. no cap. 🧬✨

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✨ SYNOPSIS ✨

augustus [parameters] --species=SPECIES queryfilename

that's the whole vibe. parameters, a species, and a query file. slay.

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🌸 OPTIONS 🌸

the mandatory option queryfilename is literally non-negotiable, she's the main character. it specifies the filename (including relative path, yes, the relative path, don't forget it 🫶) to the file containing the query sequence(s) in FASTA format.

SPECIES is an identifier for the species. use --species=help to see a list — do it, it's giving menu energy. 💅

🎀 Further parameters:

• --strand=both, --strand=forward or --strand=backward — define the strand to search on. pick your fighter.
• --genemodel=genemodel — where genemodel is one of:
  • partial — allow prediction of incomplete genes at the sequence boundaries (default, she's the baseline bestie)
  • intronless — only predict single-exon genes like in prokaryotes and some eukaryotes
  • complete — only predict complete genes
  • atleastone — predict at least one complete gene
  • exactlyone — predict exactly one complete gene
• --singlestrand=true — predict genes independently on each strand, allow overlapping genes on opposite strands. this option is turned off by default, so don't come for me if it's not doing the thing. 🙈
• --hintsfile=hintsfilename — when this option is used the prediction considering hints (extrinsic information) is turned on. hintsfilename contains the hints in gff format.
• --AUGUSTUS_CONFIG_PATH=path — path to config directory (if not specified as environment variable).
• --alternatives-from-evidence=true/false — report alternative transcripts when they are suggested by hints.
• --alternatives-from-sampling=true/false — report alternative transcripts generated through probabilistic sampling. sampling?? probabilistic?? ok genius 💀
• --maxtracks=n — for a description of these parameters see section "SAMPLING: ALTERNATIVE TRANSCRIPTS AND POSTERIOR PROBABILITIES" of docs/RUNNING-AUGUSTUS.md.
• --proteinprofile=filename — when this option is used the prediction will consider the protein profile provided as parameter. the protein profile extension is described in section "AUGUSTUS-PPX" of docs/RUNNING-AUGUSTUS.md.
• --progress=true — show a progressmeter. we love a little loading bar moment 🫶
• --gff3=on/off — output in gff3 format.
• --predictionStart=A, --predictionEnd=B — A and B define the range of the sequence for which predictions should be found.
• --UTR=on/off — predict the untranslated regions in addition to the coding sequence. this currently works only for a subset of species, so check before you get your hopes up bestie. 😭
• --noInFrameStop=true/false — do not report transcripts with in-frame stop codons. otherwise, intron-spanning stop codons could occur. default: false.
• --noprediction=true/false — if true and input is in genbank format, no prediction is made. useful for getting the annotated protein sequences.
• --uniqueGeneId=true/false — if true, output gene identifyers like this: seqname.gN.
• --paramlist — show full list of supported parameters. the whole menu, the entire buffet. 👑

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👑 AUTHORS 👑

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth. absolute icons, every single one of them. ✨

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📚 ADDITIONAL DOCUMENTATION 📚

an exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz. read it, it's giving lore. 🌈

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and that's the whole AUGUSTUS(1) manual page, bestie. the version info and the date live on that last little footer line, right where we found her — this was AUGUSTUS(1), top to bottom, and she ate. periodt. 💅💖🎀