Linux workstation

Debian 12 (Bookworm) native package

sra-toolkit

utilities for the NCBI Sequence Read Archive

Packages / Debian 12 (Bookworm) / science / sra-toolkit

[Source: sra-sdk]

Package: sra-toolkit (3.0.3+dfsg-6~deb12u1)

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [github.com]

Similar packages:

  • [libncbi-ngs3]

    Next Generation Sequencing language Bindings (full runtime)

  • [libncbi-ngs-dev]

    Next Generation Sequencing language Bindings (C++ development)

  • [libngs-c++3]

    Next Generation Sequencing language Bindings (C++ runtime)

  • [libngs-c++-dev]

    Next Generation Sequencing language Bindings (C++ development)

  • [libngs-java]

    Next Generation Sequencing language Bindings (Java bindings)

  • [libngs-java-doc]

    Next Generation Sequencing language Bindings (Java documentation)

  • [libngs-jni]

    Next Generation Sequencing language Bindings (Java native binding)

  • [python3-ngs]

    Next Generation Sequencing language Bindings (Python3 bindings)

utilities for the NCBI Sequence Read Archive

Other Packages Related to sra-toolkit:

  • dep: [libbz2-1.0]

    high-quality block-sorting file compressor library - runtime

  • dep: [libc6] (>= 2.34)

    GNU C Library: Shared libraries

  • dep: [libgcc-s1] (>= 3.0)

    GCC support library

  • dep: [libhdf5-103-1]

    HDF5 C runtime files - serial version

  • dep: [libmagic1] (>= 5.12)

    Recognize the type of data in a file using "magic" numbers - library

  • dep: [libncbi-vdb3] (>= 3.0.2+dfsg)

    libraries for using data in the INSDC Sequence Read Archives

  • dep: [libncbi-wvdb3] (>= 3.0.2+dfsg)

    virtual layer update module of ncbi-vdb library

  • dep: [libre2-9] (>= 20201101+dfsg)

    efficient, principled regular expression library

  • dep: [libssl3] (>= 3.0.0)

    Secure Sockets Layer toolkit - shared libraries

  • dep: [libstdc++6] (>= 12)

    GNU Standard C++ Library v3

  • dep: [libxml2] (>= 2.7.4)

    GNOME XML library

  • dep: [zlib1g] (>= 1:1.2.2)

    compression library - runtime

  • rec: [med-config]

    Debian Med general config package

Download sra-toolkit

ArchitecturePackage SizeInstalled SizeFiles
amd646.4 MiB17 MiB[list of files]
arm646.2 MiB18 MiB[list of files]

Package file paths (94)

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.

  • /etc/ncbi/certs.kfg
  • /etc/ncbi/debian.kfg
  • /etc/ncbi/default.kfg
  • /etc/ncbi/vdb-copy.kfg
  • /usr/bin/abi-dump
  • /usr/bin/abi-load
  • /usr/bin/align-cache
  • /usr/bin/align-info
  • /usr/bin/bam-load
  • /usr/bin/cache-mgr
  • /usr/bin/ccextract
  • /usr/bin/cg-load
  • /usr/bin/check-corrupt
  • /usr/bin/copycat
  • /usr/bin/crc32sum
  • /usr/bin/dump-blob-boundaries
  • /usr/bin/fastconv
  • /usr/bin/fasterq-dump
  • /usr/bin/fastq-dump
  • /usr/bin/fastq-load
  • /usr/bin/general-loader
  • /usr/bin/helicos-load
  • /usr/bin/illumina-dump
  • /usr/bin/illumina-load
  • /usr/bin/kar
  • /usr/bin/kar+
  • /usr/bin/kar+meta
  • /usr/bin/kdb-index
  • /usr/bin/kdbmeta
  • /usr/bin/latf-load
  • /usr/bin/make-read-filter
  • /usr/bin/md5cp
  • /usr/bin/meta-cmp
  • /usr/bin/meta-copy
  • /usr/bin/ngs-pileup
  • /usr/bin/pacbio-correct
  • /usr/bin/pacbio-load
  • /usr/bin/pacbio-loadxml
  • /usr/bin/pileup-stats
  • /usr/bin/prefetch
  • /usr/bin/rcexplain
  • /usr/bin/read-filter-redact
  • /usr/bin/ref-variation
  • /usr/bin/rowwritetest
  • /usr/bin/sam-dump
  • /usr/bin/samview
  • /usr/bin/samview-util
  • /usr/bin/schema-replace
  • /usr/bin/sff-dump
  • /usr/bin/sff-load
  • /usr/bin/sharq
  • /usr/bin/sortreadtest
  • /usr/bin/srapath
  • /usr/bin/sra-pileup
  • /usr/bin/sra-search
  • /usr/bin/sra-sort
  • /usr/bin/sra-sort-cg
  • /usr/bin/sra-stat
  • /usr/bin/srf-load
  • /usr/bin/test-download
  • /usr/bin/testld
  • /usr/bin/test-read-write-cursor
  • /usr/bin/test-sra
  • /usr/bin/txt2kdb
  • /usr/bin/var-expand
  • /usr/bin/vdb-config
  • /usr/bin/vdb-copy
  • /usr/bin/vdb-decrypt
  • /usr/bin/vdb-diff
  • /usr/bin/vdb-dump
  • /usr/bin/vdb-encrypt
  • /usr/bin/vdb-lock
  • /usr/bin/vdb-sql
  • /usr/bin/vdb-unlock
  • /usr/bin/vdb-validate
  • /usr/lib/debian-med/bin/kget
  • /usr/lib/sra-toolkit/fasterq-dump-orig
  • /usr/lib/sra-toolkit/fastq-dump-orig
  • /usr/lib/sra-toolkit/prefetch-orig
  • /usr/lib/sra-toolkit/sam-dump-orig
  • /usr/lib/sra-toolkit/srapath-orig
  • /usr/lib/sra-toolkit/sra-pileup-orig
  • /usr/lib/sra-toolkit/sratools
  • /usr/lib/sra-toolkit/vdb-dump-orig
  • /usr/share/doc/sra-toolkit/changelog.Debian.gz
  • /usr/share/doc/sra-toolkit/changelog.gz
  • /usr/share/doc/sra-toolkit/copyright
  • /usr/share/doc/sra-toolkit/README-blastn
  • /usr/share/doc/sra-toolkit/README.Debian
  • /usr/share/doc/sra-toolkit/README.md.gz
  • /usr/share/doc/sra-toolkit/README.test
  • /usr/share/doc/sra-toolkit/README-vdb-config.gz
  • /usr/share/doc/sra-toolkit/run-unit-test
  • /usr/share/doc/sra-toolkit/test-data.tar.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 browserBuild an image that includes sra-toolkit

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.

VersionReleaseArchitectureRepositoryPackage sizeInstalled sizePublisher repository artifact
3.0.3+dfsg-6~deb12u1bookworm / mainamd64Debian 12 · main · amd646.4 MiB17 MiBpool/main/s/sra-sdk/sra-toolkit_3.0.3+dfsg-6~deb12u1_amd64.deb
3.0.3+dfsg-6~deb12u1bookworm / mainarm64Debian 12 · main · arm646.2 MiB18 MiBpool/main/s/sra-sdk/sra-toolkit_3.0.3+dfsg-6~deb12u1_arm64.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.

3.0.3+dfsg-6~deb12u1 / 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: e58bbbf503590c2a4cfdf98da42066330723aa6e46be95fd2b77c758fcbabce0

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

printf '%s %s\n' 'e58bbbf503590c2a4cfdf98da42066330723aa6e46be95fd2b77c758fcbabce0' 'sra-toolkit_3.0.3+dfsg-6~deb12u1_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

3.0.3+dfsg-6~deb12u1 / 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: 24e8affeffaf4c5994275932cef47a00ae304561bdc0477373728c25c568cd30

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

printf '%s %s\n' '24e8affeffaf4c5994275932cef47a00ae304561bdc0477373728c25c568cd30' 'sra-toolkit_3.0.3+dfsg-6~deb12u1_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

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 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 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

sra-toolkit Package for Debian 12 (Bookworm) | OpenFactory