Install augustus with Homebrew, apt, Nix, pacman

Project links

• Homepage
• Repository

Commands and aliases

• aln2wig
• augustus
• bam2hints
• bam2wig
• compileSpliceCands
• etraining
• fastBlockSearch
• filterBam
• homGeneMapping
• joingenes
• pp_simScore
• prepareAlign

Project history

The University of Greifswald project site identifies AUGUSTUS as a program for predicting genes in eukaryotic genomic sequences and carries 2003 metadata. The official reference list traces the research lineage from Mario Stanke's 2003 hidden-Markov-model work through the 2004 AUGUSTUS web-server paper and later papers on hints, alternative transcripts, cDNA alignments, and comparative gene prediction.

The current GitHub README says AUGUSTUS can find genes and gene structures in one or more genomes, can run ab initio, and can incorporate hints from EST, protein alignments, MS/MS, and syntenic genomic alignments. The ABOUT document notes that since version 3.0 it can predict genes simultaneously in several aligned genomes.

The project site records several adoption-era milestones: an automatic annotation pipeline was distributed by 2009, RNA-Seq integration was documented in 2012, and source-code issue handling moved to GitHub. Releases on GitHub include 3.3.2 in 2018, 3.3.3 in 2019, 3.4.0 in 2020, and 3.5.0 in 2022.

Adoption history

AUGUSTUS adoption is driven by genome annotation workflows rather than casual CLI use. The official site offers web interfaces, a larger WebAUGUSTUS service, local downloads, training, species parameter sets, and links to accuracy results. The supplied package-manager facts show Homebrew, Debian, Nix, Arch, and Ubuntu packages, reflecting its role as a reproducible command-line dependency in bioinformatics environments.

How it is used

The official running guide describes the basic command as augustus [parameters] --species=SPECIES queryfilename, with uncompressed FASTA input and GTF-like output. Users choose species parameter sets, redirect output to GFF/GTF files, pass hints files and extrinsic configuration, retrain species parameters, and run auxiliary programs such as etraining and bam2hints.

Why package nerds care

AUGUSTUS is package-interesting because the executable alone is not enough: the config directory, species parameters, extrinsic.cfg, scripts, examples, and auxiliary programs must line up with AUGUSTUS_CONFIG_PATH or the executable-relative ../config fallback. It is a classic scientific package where data files, environment variables, and compiled tools are one deployable unit.

Timeline

• 2003: Foundational HMM gene-prediction thesis and related Bioinformatics paper appeared.
• 2004: AUGUSTUS web-server paper was published.
• 2006: Papers covered alternative transcripts and extrinsic hints.
• 2008: cDNA and syntenic alignment improvements were published.
• 2009: The project site announced an automatic annotation pipeline for download.
• 2012: RNA-Seq integration for the download version was documented.
• 2016: Multi-genome gene finding was published.
• 2018: GitHub release 3.3.2 was published.
• 2022: GitHub release 3.5.0 was published.

Related projects

• AUGUSTUS is commonly discussed with WebAUGUSTUS, BRAKER, comparative gene prediction workflows, RNA-Seq hint generation, genome browsers such as Gbrowse, and the broader University of Greifswald bioinformatics toolchain.

Sources

• https://api.github.com/repos/Gaius-Augustus/Augustus
• https://bioinf.uni-greifswald.de/augustus
• https://github.com/Gaius-Augustus/Augustus/blob/master/README.md
• https://github.com/Gaius-Augustus/Augustus/blob/master/docs/ABOUT.md
• https://github.com/Gaius-Augustus/Augustus/blob/master/docs/REFERENCES.md
• https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md