Debian 12 (Bookworm) native package

abyss

de novo, parallel, sequence assembler for short reads

Packages / Debian 12 (Bookworm) / science / abyss

Package: abyss (2.3.5+dfsg-2)

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [github.com]

de novo, parallel, sequence assembler for short reads

Other Packages Related to abyss:

dep: [make]
utility for directing compilation
dep: [libc6] (>= 2.34)
GNU C Library: Shared libraries
dep: [libgcc-s1] (>= 3.0)
GCC support library
dep: [libgomp1] (>= 4.9)
GCC OpenMP (GOMP) support library
dep: [libopenmpi3] (>= 4.1.4)
high performance message passing library -- shared library
dep: [libsqlite3-0] (>= 3.5.9)
SQLite 3 shared library
dep: [libstdc++6] (>= 12)
GNU Standard C++ Library v3
dep: [perl] [any]
Larry Wall's Practical Extraction and Report Language
dep: [bsdextrautils]
extra utilities from 4.4BSD-Lite
dep: [openmpi-common]
high performance message passing library -- common files
dep: [openmpi-bin]
high performance message passing library -- binaries

Download abyss

Architecture	Package Size	Installed Size	Files
amd64	3.0 MiB	9.4 MiB	[list of files]
arm64	2.8 MiB	9.9 MiB	[list of files]

Rutas de archivos del paquete (76)

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/abyss-fixmate
/usr/bin/abyss-pe
/usr/bin/DistanceEst
/usr/lib/abyss/ABYSS
/usr/lib/abyss/abyss-align
/usr/lib/abyss/abyss-bloom
/usr/lib/abyss/abyss-bloom-dbg
/usr/lib/abyss/abyss-bloom-dist.mk
/usr/lib/abyss/abyss-bowtie
/usr/lib/abyss/abyss-bowtie2
/usr/lib/abyss/abyss-bwa
/usr/lib/abyss/abyss-bwamem
/usr/lib/abyss/abyss-bwasw
/usr/lib/abyss/abyss-db-csv
/usr/lib/abyss/abyss-db-txt
/usr/lib/abyss/abyss-dida
/usr/lib/abyss/abyss-fac
/usr/lib/abyss/abyss-fatoagp
/usr/lib/abyss/abyss-filtergraph
/usr/lib/abyss/abyss-fixmate
/usr/lib/abyss/abyss-fixmate-ssq
/usr/lib/abyss/abyss-gapfill
/usr/lib/abyss/abyss-gc
/usr/lib/abyss/abyss-index
/usr/lib/abyss/abyss-junction
/usr/lib/abyss/abyss-kaligner
/usr/lib/abyss/abyss-layout
/usr/lib/abyss/abyss-longseqdist
/usr/lib/abyss/abyss-map
/usr/lib/abyss/abyss-map-ssq
/usr/lib/abyss/abyss-mergepairs
/usr/lib/abyss/abyss-overlap
/usr/lib/abyss/ABYSS-P
/usr/lib/abyss/abyss-paired-dbg
/usr/lib/abyss/abyss-paired-dbg-mpi
/usr/lib/abyss/abyss-pe
/usr/lib/abyss/abyss-rresolver-short
/usr/lib/abyss/abyss-samtoafg
/usr/lib/abyss/abyss-scaffold
/usr/lib/abyss/abyss-sealer
/usr/lib/abyss/abyss-stack-size
/usr/lib/abyss/abyss-tabtomd
/usr/lib/abyss/abyss-todot
/usr/lib/abyss/abyss-tofastq
/usr/lib/abyss/AdjList
/usr/lib/abyss/Consensus
/usr/lib/abyss/DAssembler
/usr/lib/abyss/DistanceEst
/usr/lib/abyss/DistanceEst-ssq
/usr/lib/abyss/KAligner
/usr/lib/abyss/konnector
/usr/lib/abyss/logcounter
/usr/lib/abyss/MergeContigs
/usr/lib/abyss/MergePaths
/usr/lib/abyss/Overlap
/usr/lib/abyss/ParseAligns
/usr/lib/abyss/PathConsensus
/usr/lib/abyss/PathOverlap
/usr/lib/abyss/PopBubbles
/usr/lib/abyss/SimpleGraph
/usr/share/doc/abyss/changelog.Debian.gz
/usr/share/doc/abyss/changelog.gz
/usr/share/doc/abyss/CITATION.bib
/usr/share/doc/abyss/CITATION.md
/usr/share/doc/abyss/copyright
/usr/share/doc/abyss/flowchart.pdf.gz
/usr/share/doc/abyss/flowchart_simplified.pdf.gz
/usr/share/doc/abyss/README.html
/usr/share/doc/abyss/README.md.gz
/usr/share/doc/abyss/README.test
/usr/share/doc/abyss/run-unit-test
/usr/share/doc/abyss/test-data/reads1.fastq.gz
/usr/share/doc/abyss/test-data/reads2.fastq.gz
/usr/share/doc-base/abyss.abyss-flowcharts
/usr/share/man/man1/abyss-fixmate.1.gz
/usr/share/man/man1/DistanceEst.1.gz

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

Usar este paquete

OpenFactory puede arrancar este sistema operativo en una máquina virtual del navegador, o iniciar una construcción que incluye el nombre nativo del paquete de este registro.

Probar Debian 12 (Bookworm) en el navegador Construir una imagen que incluye abyss

Versiones, suites y repositorios

Cada fila es metadato del índice de paquetes para una versión, arquitectura, suite y repositorio. Nombres, URL y tamaños vienen de la fuente; un enlace es un punto de descarga que puede cambiar, no una redistribución de OpenFactory.

Version	Release	Architecture	Repository	Package size	Installed size	Publisher repository artifact
2.3.5+dfsg-2	bookworm / main	amd64	Debian 12 · main · amd64	3.0 MiB	9.4 MiB	pool/main/a/abyss/abyss_2.3.5+dfsg-2_amd64.deb
2.3.5+dfsg-2	bookworm / main	arm64	Debian 12 · main · arm64	2.8 MiB	9.9 MiB	pool/main/a/abyss/abyss_2.3.5+dfsg-2_arm64.deb

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

Sumas de comprobación y fechas de observación

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.

2.3.5+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: 40885570a890d912e86d8c9eac295aab80b0c09cb5a40792809620b8df49e696

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

printf '%s  %s\n' '40885570a890d912e86d8c9eac295aab80b0c09cb5a40792809620b8df49e696' 'abyss_2.3.5+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

2.3.5+dfsg-2 / arm64Observed 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: 61f20f06f4fcc6f95dee8b350b9787477daa63d47526dce2d16d24e49498ef6d

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

printf '%s  %s\n' '61f20f06f4fcc6f95dee8b350b9787477daa63d47526dce2d16d24e49498ef6d' 'abyss_2.3.5+dfsg-2_arm64.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 arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00

Completitud del registro

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

Fuentes y procedencia

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