Debian 12 (Bookworm) native package

augustus

gene prediction in eukaryotic genomes

Packages / Debian 12 (Bookworm) / science / augustus

Package: augustus (3.5.0+dfsg-2)

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [bioinf.uni-greifswald.de]

gene prediction in eukaryotic genomes

Other Packages Related to augustus:

dep: [libbamtools2.5.2] (>= 2.5.2+dfsg)
dynamic library for manipulating BAM (genome alignment) files
dep: [libboost-iostreams1.74.0] (>= 1.74.0)
Boost.Iostreams Library
dep: [libc6] (>= 2.34)
GNU C Library: Shared libraries
dep: [libcolamd2] (>= 1:4.5.2)
column approximate minimum degree ordering library for sparse matrices
dep: [libgcc-s1] (>= 3.0)
GCC support library
dep: [libgsl27] (>= 2.7.1)
GNU Scientific Library (GSL) -- library package
dep: [libhts3] (>= 1.10)
C library for high-throughput sequencing data formats
dep: [libmariadb3] (>= 3.0.0)
MariaDB database client library
dep: [libmysql++3v5] (>= 3.2.5-1~)
MySQL C++ library bindings (runtime)
dep: [libsqlite3-0] (>= 3.5.9)
SQLite 3 shared library
dep: [libstdc++6] (>= 11)
GNU Standard C++ Library v3
dep: [augustus-data]
data files for AUGUSTUS

rec: [samtools]
processing sequence alignments in SAM, BAM and CRAM formats

sug: [cdbfasta]
Constant DataBase indexing and retrieval tools for multi-FASTA files
sug: [diamond-aligner]
accelerated BLAST compatible local sequence aligner
sug: [libfile-which-perl]
Perl module for searching paths for executable programs
sug: [libparallel-forkmanager-perl]
simple parallel processing fork manager for Perl
sug: [libyaml-perl]
YAML Ain't Markup Language
sug: [libdbd-mysql-perl]
Perl5 database interface to the MariaDB/MySQL database
sug: [python3-biopython]
Python3 library for bioinformatics

Download augustus

Architecture	Package Size	Installed Size	Files
amd64	2.0 MiB	11 MiB	[list of files]

Package file paths (142)

Paths come from the repository package-file index for the observed builds. They describe archive/package associations, not every file that will exist on a running system after maintainer scripts, alternatives, generated state, diversions, or installation choices.

/usr/bin/aln2wig
/usr/bin/augustus
/usr/bin/bam2hints
/usr/bin/bam2wig
/usr/bin/compileSpliceCands
/usr/bin/etraining
/usr/bin/fastBlockSearch
/usr/bin/filterBam
/usr/bin/getSeq
/usr/bin/homGeneMapping
/usr/bin/joingenes
/usr/bin/load2db
/usr/bin/load2sqlitedb
/usr/bin/pp_simScore
/usr/bin/prepareAlign
/usr/share/augustus/scripts/aa2nonred.pl
/usr/share/augustus/scripts/add_name_to_gff3.pl
/usr/share/augustus/scripts/augustify.py
/usr/share/augustus/scripts/augustus2browser.pl
/usr/share/augustus/scripts/augustus2gbrowse.pl
/usr/share/augustus/scripts/autoAug.pl
/usr/share/augustus/scripts/autoAugPred.pl
/usr/share/augustus/scripts/autoAugTrain.pl
/usr/share/augustus/scripts/bamToWig.py
/usr/share/augustus/scripts/bedgraph2wig.pl
/usr/share/augustus/scripts/blat2gbrowse.pl
/usr/share/augustus/scripts/blat2hints.pl
/usr/share/augustus/scripts/block2prfl.pl
/usr/share/augustus/scripts/cegma2gff.pl
/usr/share/augustus/scripts/checkParamArchive.pl
/usr/share/augustus/scripts/checkUTR
/usr/share/augustus/scripts/cleanDOSfasta.pl
/usr/share/augustus/scripts/clusterAndSplitGenes.pl
/usr/share/augustus/scripts/compare_masking.pl
/usr/share/augustus/scripts/computeFlankingRegion.pl
/usr/share/augustus/scripts/createAugustusJoblist.pl
/usr/share/augustus/scripts/del_from_prfl.pl
/usr/share/augustus/scripts/evalCGP.pl
/usr/share/augustus/scripts/eval_dualdecomp.pl
/usr/share/augustus/scripts/eval_multi_gtf.pl
/usr/share/augustus/scripts/exonerate2hints.pl
/usr/share/augustus/scripts/exoniphyDb2hints.pl
/usr/share/augustus/scripts/extractAnno.py
/usr/share/augustus/scripts/extractTranscriptEnds.pl
/usr/share/augustus/scripts/filterGenesIn_mRNAname.pl
/usr/share/augustus/scripts/filterGenesIn.pl
/usr/share/augustus/scripts/filterGenesOut_mRNAname.pl
/usr/share/augustus/scripts/filterGenes.pl
/usr/share/augustus/scripts/filterInFrameStopCodons.pl
/usr/share/augustus/scripts/filterMaf.pl
/usr/share/augustus/scripts/filter-ppx.pl
/usr/share/augustus/scripts/filterPSL.pl
/usr/share/augustus/scripts/filterShrimp.pl
/usr/share/augustus/scripts/filterSpliceHints.pl
/usr/share/augustus/scripts/findGffNamesInFasta.pl
/usr/share/augustus/scripts/findRepetitiveProtSeqs.py
/usr/share/augustus/scripts/fix_in_frame_stop_codon_genes.py
/usr/share/augustus/scripts/fix_joingenes_gtf.pl
/usr/share/augustus/scripts/gbrowse.conf
/usr/share/augustus/scripts/gbrowseold2gff3.pl
/usr/share/augustus/scripts/gbSmallDNA2gff.pl
/usr/share/augustus/scripts/getAnnoFastaFromJoingenes.py
/usr/share/augustus/scripts/getAnnoFasta.pl
/usr/share/augustus/scripts/getLinesMatching.pl
/usr/share/augustus/scripts/get_loci_from_gb.pl
/usr/share/augustus/scripts/gff2gbSmallDNA.pl
/usr/share/augustus/scripts/gff2ps_mycustom
/usr/share/augustus/scripts/gffGetmRNA.pl
/usr/share/augustus/scripts/gp2othergp.pl
/usr/share/augustus/scripts/gtf2aa.pl
/usr/share/augustus/scripts/gtf2bed.pl
/usr/share/augustus/scripts/gtf2gff.pl
/usr/share/augustus/scripts/gth2gtf.pl
/usr/share/augustus/scripts/hal2maf_split.pl
/usr/share/augustus/scripts/helpMod.pm
/usr/share/augustus/scripts/join_aug_pred.pl
/usr/share/augustus/scripts/join_mult_hints.pl
/usr/share/augustus/scripts/joinPeptides.pl
/usr/share/augustus/scripts/maf2conswig.pl
/usr/share/augustus/scripts/makeMatchLists.pl
/usr/share/augustus/scripts/makeUtrTrainingSet.pl
/usr/share/augustus/scripts/maskNregions.pl
/usr/share/augustus/scripts/merge_masking.pl
/usr/share/augustus/scripts/moveParameters.pl
/usr/share/augustus/scripts/msa2prfl.pl
/usr/share/augustus/scripts/new_species.pl
/usr/share/augustus/scripts/optimize_augustus.pl
/usr/share/augustus/scripts/opt_init_and_term_probs.pl
/usr/share/augustus/scripts/parseSim4Output.pl
/usr/share/augustus/scripts/partition_gtf2gb.pl
/usr/share/augustus/scripts/pasapolyA2hints.pl
/usr/share/augustus/scripts/peptides2alternatives.pl
/usr/share/augustus/scripts/peptides2hints.pl
/usr/share/augustus/scripts/phastconsDB2hints.pl
/usr/share/augustus/scripts/polyA2hints.pl
/usr/share/augustus/scripts/prints2prfl.pl
/usr/share/augustus/scripts/pslMap.pl
/usr/share/augustus/scripts/randomSplit.pl
/usr/share/augustus/scripts/README.autoAug
/usr/share/augustus/scripts/rename_species.pl
/usr/share/augustus/scripts/retroDB2hints.pl
/usr/share/augustus/scripts/rmRedundantHints.pl
/usr/share/augustus/scripts/runAllSim4.pl
/usr/share/augustus/scripts/samMap.pl
/usr/share/augustus/scripts/scipiogff2gff.pl
/usr/share/augustus/scripts/setStopCodonFreqs.pl
/usr/share/augustus/scripts/simpleFastaHeaders.pl
/usr/share/augustus/scripts/simplifyFastaHeaders.pl
/usr/share/augustus/scripts/SplicedAlignment.pm
/usr/share/augustus/scripts/splitMfasta.pl
/usr/share/augustus/scripts/split_wiggle.pl
/usr/share/augustus/scripts/stringtie2fa.py
/usr/share/augustus/scripts/summarizeACGTcontent.pl
/usr/share/augustus/scripts/transMap2hints.pl
/usr/share/augustus/scripts/uniquePeptides.pl
/usr/share/augustus/scripts/utrgff2gbrowse.pl
/usr/share/augustus/scripts/webserver-results.head
/usr/share/augustus/scripts/webserver-results.tail
/usr/share/augustus/scripts/weedMaf.pl
/usr/share/augustus/scripts/wig2hints.pl
/usr/share/augustus/scripts/wigchoose.pl
/usr/share/augustus/scripts/writeResultsPage.pl
/usr/share/augustus/scripts/yaml2gff.1.4.pl
/usr/share/doc/augustus/changelog.Debian.gz
/usr/share/doc/augustus/changelog.gz
/usr/share/doc/augustus/copyright
/usr/share/doc/augustus/HISTORY.TXT.gz
/usr/share/man/man1/aln2wig.1.gz
/usr/share/man/man1/augustus.1.gz
/usr/share/man/man1/bam2hints.1.gz
/usr/share/man/man1/bam2wig.1.gz
/usr/share/man/man1/compileSpliceCands.1.gz
/usr/share/man/man1/etraining.1.gz
/usr/share/man/man1/fastBlockSearch.1.gz
/usr/share/man/man1/filterBam.1.gz
/usr/share/man/man1/getSeq.1.gz
/usr/share/man/man1/homGeneMapping.1.gz
/usr/share/man/man1/joingenes.1.gz
/usr/share/man/man1/load2db.1.gz
/usr/share/man/man1/load2sqlitedb.1.gz
/usr/share/man/man1/pp_simScore.1.gz
/usr/share/man/man1/prepareAlign.1.gz

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

Use this package

OpenFactory can boot this operating system in a browser VM, or start a build that includes the native package name from this record.

Try Debian 12 (Bookworm) in the browser Build an image that includes augustus

Versions, suites, and repositories

Each row is recorded package-index metadata for one version, architecture, suite, and repository. Names, URLs, and sizes are source-reported; a link is a potentially mutable retrieval location, not an OpenFactory redistribution claim or proof that OpenFactory retained the artifact bytes.

Version	Release	Architecture	Repository	Package size	Installed size	Publisher repository artifact
3.5.0+dfsg-2	bookworm / main	amd64	Debian 12 · main · amd64	2.0 MiB	11 MiB	pool/main/a/augustus/augustus_3.5.0+dfsg-2_amd64.deb

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

Checksums and observation dates

For an APT source, signature verification authenticates the repository metadata chain and the Packages index containing this source-reported artifact digest. It does not certify package safety.

3.5.0+dfsg-2 / amd64Observed Sep 1, 2026 to Sep 1, 2026

Verification status: Metadata observed; artifact bytes were not independently fetched or hashed by this catalog import. The digest below is source-reported.

Source-reported sha256: c97b2e1008beb62c3cff07fba32ada8adf5c9dffdabb18438ab9e69532f70d76

After downloading that exact artifact, compare its bytes with the source-reported expected digest:

printf '%s  %s\n' 'c97b2e1008beb62c3cff07fba32ada8adf5c9dffdabb18438ab9e69532f70d76' 'augustus_3.5.0+dfsg-2_amd64.deb' | sha256sum --check --strict -

A match establishes equality with the repository metadata value. It does not establish safety or catalog-side artifact retrieval.

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

Catalog record completeness

The completeness score measures metadata coverage, not software quality, security, compatibility, or suitability.

Summary and description: 25/25
Artifact path and source digest: 25/25
Dependency metadata: 15/15
Package-file index: 15/15
Homepage: 5/5
License text: 0/5
Source package or maintainer: 10/10

Recorded total: 95/100

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5, Debian 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00. The cross-OS mapping is catalog-derived from the source-reported homepage; it does not establish authorship or publisher identity

Sources and provenance

Field-source links above resolve here. Each source entry names the metadata publisher, trust tier, exact snapshot revision, signature result, and observation time; catalog-derived mappings are labeled separately.

Debian 12 (Bookworm) main amd64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-amd64/Packages.xz
Expected SHA-256: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Observed SHA-256: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Result: match verified
Debian 12 (Bookworm) main arm64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-arm64/Packages.xz
Expected SHA-256: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Observed SHA-256: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Result: match verified