Debian 13 (Trixie) native package

spades

genome assembler for single-cell and isolates data sets

Packages / Debian 13 (Trixie) / science / spades

Package: spades (4.0.0+really3.15.5+dfsg-1)

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [github.com]

genome assembler for single-cell and isolates data sets

Other Packages Related to spades:

dep: [libc6] (>= 2.38)
GNU C Library: Shared libraries
dep: [libgcc-s1] (>= 4.0)
GCC support library
dep: [libgomp1] (>= 6)
GCC OpenMP (GOMP) support library
dep: [libnlopt0] (>= 2.6.1)
nonlinear optimization library
dep: [libssw0] (>= 1.1)
fast SIMD parallelized implementation of the Smith-Waterman algorithm
dep: [libstdc++6] (>= 14)
GNU Standard C++ Library v3
dep: [zlib1g] (>= 1:1.2.3.3)
compression library - runtime
dep: [python3] [any]
interactive high-level object-oriented language (default python3 version)
dep: [python3]
interactive high-level object-oriented language (default python3 version)
dep: [python3-joblib]
tools to provide lightweight pipelining in Python
dep: [python3-packaging]
core utilities for python3 packages
dep: [python3-yaml]
YAML parser and emitter for Python3
dep: [bwa]
Burrows-Wheeler Aligner
dep: [bamtools]
toolkit for manipulating BAM (genome alignment) files
dep: [samtools]
processing sequence alignments in SAM, BAM and CRAM formats

Download spades

Architecture	Package Size	Installed Size	Files
amd64	8.8 MiB	39 MiB	[list of files]

Шляхи файлів пакета (175)

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/coronaspades
/usr/bin/coronaspades.py
/usr/bin/metaspades
/usr/bin/metaspades.py
/usr/bin/plasmidspades
/usr/bin/plasmidspades.py
/usr/bin/rnaspades
/usr/bin/rnaspades.py
/usr/bin/spades
/usr/bin/spades.py
/usr/bin/truspades
/usr/bin/truspades.py
/usr/libexec/spades/cds-mapping-stats
/usr/libexec/spades/cds-subgraphs
/usr/libexec/spades/coronaspades.py
/usr/libexec/spades/mag-improve
/usr/libexec/spades/metaplasmidspades.py
/usr/libexec/spades/metaspades.py
/usr/libexec/spades/metaviralspades.py
/usr/libexec/spades/plasmidspades.py
/usr/libexec/spades/rnaspades.py
/usr/libexec/spades/rnaviralspades.py
/usr/libexec/spades/spades-bwa
/usr/libexec/spades/spades-convert-bin-to-fasta
/usr/libexec/spades/spades-core
/usr/libexec/spades/spades-corrector-core
/usr/libexec/spades/spades-gbuilder
/usr/libexec/spades/spades-gmapper
/usr/libexec/spades/spades-gsimplifier
/usr/libexec/spades/spades-hammer
/usr/libexec/spades/spades_init.py
/usr/libexec/spades/spades-ionhammer
/usr/libexec/spades/spades-kmercount
/usr/libexec/spades/spades-kmer-estimating
/usr/libexec/spades/spades.py
/usr/libexec/spades/spades-read-filter
/usr/libexec/spades/spades-truseq-scfcorrection
/usr/libexec/spades/spaligner
/usr/libexec/spades/truspades.py
/usr/libexec/spades/VERSION
/usr/share/doc/spades/changelog.Debian.gz
/usr/share/doc/spades/changelog.gz
/usr/share/doc/spades/copyright
/usr/share/doc/spades/examples/configs/careful_mda_mode.info
/usr/share/doc/spades/examples/configs/careful_mode.info
/usr/share/doc/spades/examples/configs/config.info
/usr/share/doc/spades/examples/configs/construction.info
/usr/share/doc/spades/examples/configs/detail_info_printer.info
/usr/share/doc/spades/examples/configs/distance_estimation.info
/usr/share/doc/spades/examples/configs/hmm_mode.info
/usr/share/doc/spades/examples/configs/isolate_mode.info
/usr/share/doc/spades/examples/configs/large_genome_mode.info
/usr/share/doc/spades/examples/configs/mda_mode.info
/usr/share/doc/spades/examples/configs/meta_mode.info
/usr/share/doc/spades/examples/configs/metaplasmid_mode.info
/usr/share/doc/spades/examples/configs/metaviral_mode.info
/usr/share/doc/spades/examples/configs/pe_params.info
/usr/share/doc/spades/examples/configs/plasmid_mode.info
/usr/share/doc/spades/examples/configs/README
/usr/share/doc/spades/examples/configs/rna_mode.info
/usr/share/doc/spades/examples/configs/rnaviral_mode.info
/usr/share/doc/spades/examples/configs/sewage_mode.info
/usr/share/doc/spades/examples/configs/simplification.info
/usr/share/doc/spades/examples/configs/toy.info
/usr/share/doc/spades/NEWS.Debian.gz
/usr/share/doc/spades/README.md.gz
/usr/share/doc/spades/README.test
/usr/share/doc/spades/run-unit-test
/usr/share/lintian/overrides/spades
/usr/share/man/man1/coronaspades.1.gz
/usr/share/man/man1/coronaspades.py.1.gz
/usr/share/man/man1/metaspades.1.gz
/usr/share/man/man1/metaspades.py.1.gz
/usr/share/man/man1/plasmidspades.1.gz
/usr/share/man/man1/plasmidspades.py.1.gz
/usr/share/man/man1/rnaspades.1.gz
/usr/share/man/man1/rnaspades.py.1.gz
/usr/share/man/man1/spades.1.gz
/usr/share/man/man1/spades.py.1.gz
/usr/share/man/man1/truspades.1.gz
/usr/share/man/man1/truspades.py.1.gz
/usr/share/python3/runtime.d/spades.rtupdate
/usr/share/spades/biosynthetic_spades_hmms/AMP.hmm.gz
/usr/share/spades/biosynthetic_spades_hmms/AT.hmm.gz
/usr/share/spades/biosynthetic_spades_hmms/CStart.hmm.gz
/usr/share/spades/biosynthetic_spades_hmms/KR.hmm.gz
/usr/share/spades/biosynthetic_spades_hmms/KS.hmm.gz
/usr/share/spades/biosynthetic_spades_hmms/TE.hmm.gz
/usr/share/spades/configs/corrector/corrector.info
/usr/share/spades/configs/debruijn/careful_mda_mode.info
/usr/share/spades/configs/debruijn/careful_mode.info
/usr/share/spades/configs/debruijn/config.info
/usr/share/spades/configs/debruijn/construction.info
/usr/share/spades/configs/debruijn/detail_info_printer.info
/usr/share/spades/configs/debruijn/distance_estimation.info
/usr/share/spades/configs/debruijn/hmm_mode.info
/usr/share/spades/configs/debruijn/isolate_mode.info
/usr/share/spades/configs/debruijn/large_genome_mode.info
/usr/share/spades/configs/debruijn/mda_mode.info
/usr/share/spades/configs/debruijn/meta_mode.info
/usr/share/spades/configs/debruijn/metaplasmid_mode.info
/usr/share/spades/configs/debruijn/metaviral_mode.info
/usr/share/spades/configs/debruijn/moleculo_mode.info
/usr/share/spades/configs/debruijn/pe_params.info
/usr/share/spades/configs/debruijn/plasmid_mode.info
/usr/share/spades/configs/debruijn/rna_mode.info
/usr/share/spades/configs/debruijn/rnaviral_mode.info
/usr/share/spades/configs/debruijn/simplification.info
/usr/share/spades/configs/debruijn/toy.info
/usr/share/spades/configs/debruijn/tsa.info
/usr/share/spades/configs/hammer/config.info
/usr/share/spades/configs/ionhammer/ionhammer.cfg
/usr/share/spades/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz
/usr/share/spades/coronaspades_hmms/Phan-CoV.hmm.gz
/usr/share/spades/spades_pipeline/commands_parser.py
/usr/share/spades/spades_pipeline/common/alignment.py
/usr/share/spades/spades_pipeline/common/__init__.py
/usr/share/spades/spades_pipeline/common/parallel_launcher.py
/usr/share/spades/spades_pipeline/common/sam_parser.py
/usr/share/spades/spades_pipeline/common/SeqIO.py
/usr/share/spades/spades_pipeline/executors/executor_local.py
/usr/share/spades/spades_pipeline/executors/executor_save_yaml.py
/usr/share/spades/spades_pipeline/executors/executors.py
/usr/share/spades/spades_pipeline/options_parser.py
/usr/share/spades/spades_pipeline/options_storage.py
/usr/share/spades/spades_pipeline/process_cfg.py
/usr/share/spades/spades_pipeline/run_contig_breaker.py
/usr/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py
/usr/share/spades/spades_pipeline/scripts/check_test_script.py
/usr/share/spades/spades_pipeline/scripts/compress_all.py
/usr/share/spades/spades_pipeline/scripts/copy_files.py
/usr/share/spades/spades_pipeline/scripts/correction_iteration_script.py
/usr/share/spades/spades_pipeline/scripts/plasmid_glue.py
/usr/share/spades/spades_pipeline/scripts/postprocessing_script.py
/usr/share/spades/spades_pipeline/scripts/preprocess_contigs.py
/usr/share/spades/spades_pipeline/scripts/preprocess_interlaced_reads.py
/usr/share/spades/spades_pipeline/stages/before_start_stage.py
/usr/share/spades/spades_pipeline/stages/breaking_scaffolds_stage.py
/usr/share/spades/spades_pipeline/stages/check_test_stage.py
/usr/share/spades/spades_pipeline/stages/correction_stage.py
/usr/share/spades/spades_pipeline/stages/error_correction_stage.py
/usr/share/spades/spades_pipeline/stages/__init__.py
/usr/share/spades/spades_pipeline/stages/pipeline.py
/usr/share/spades/spades_pipeline/stages/postprocessing_stage.py
/usr/share/spades/spades_pipeline/stages/preprocess_reads_stage.py
/usr/share/spades/spades_pipeline/stages/spades_iteration_stage.py
/usr/share/spades/spades_pipeline/stages/spades_stage.py
/usr/share/spades/spades_pipeline/stages/stage.py
/usr/share/spades/spades_pipeline/stages/terminating_stage.py
/usr/share/spades/spades_pipeline/support.py
/usr/share/spades/spades_pipeline/truspades/barcode_extraction.py
/usr/share/spades/spades_pipeline/truspades/break_by_coverage.py
/usr/share/spades/spades_pipeline/truspades/generate_quality.py
/usr/share/spades/spades_pipeline/truspades/id_generation.py
/usr/share/spades/spades_pipeline/truspades/__init__.py
/usr/share/spades/spades_pipeline/truspades/launch_options.py
/usr/share/spades/spades_pipeline/truspades/moleculo_filter_contigs.py
/usr/share/spades/spades_pipeline/truspades/moleculo_postprocessing.py
/usr/share/spades/spades_pipeline/truspades/reference_construction.py
/usr/share/spades/spades_pipeline/truspades/string_dist_utils.py
/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz
/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz
/usr/share/spades/test_dataset/genes_1K.gff
/usr/share/spades/test_dataset/genes_1K.txt
/usr/share/spades/test_dataset/operons_1K.gff
/usr/share/spades/test_dataset/operons_1K.txt
/usr/share/spades/test_dataset_plasmid/pl1.fq.gz
/usr/share/spades/test_dataset_plasmid/pl2.fq.gz
/usr/share/spades/test_dataset/reference_1K.fa.gz
/usr/share/spades/test_dataset_truspades/A_R1.fastq.gz
/usr/share/spades/test_dataset_truspades/A_R2.fastq.gz
/usr/share/spades/test_dataset_truspades/B_R1.fastq.gz
/usr/share/spades/test_dataset_truspades/B_R2.fastq.gz
/usr/share/spades/VERSION
/usr/share/spaligner/spaligner_config.yaml

Field source: Debian 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3

Використати цей пакет

OpenFactory може завантажити цю операційну систему у віртуальній машині браузера або почати збірку образу з рідною назвою пакета з цього запису.

Спробувати Debian 13 (Trixie) у браузері Зібрати образ, що містить spades

Версії, набори та репозиторії

Кожен рядок: метадані індексу пакетів для однієї версії, архітектури, набору й репозиторію. Назви, URL і розміри зі джерела; посилання є змінним місцем отримання, не перерозповсюдженням OpenFactory.

Version	Release	Architecture	Repository	Package size	Installed size	Publisher repository artifact
4.0.0+really3.15.5+dfsg-1	trixie / main	amd64	Debian 13 · main · amd64	8.8 MiB	39 MiB	pool/main/s/spades/spades_4.0.0+really3.15.5+dfsg-1_amd64.deb

Field source: Debian 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3

Контрольні суми й дати спостереження

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.

4.0.0+really3.15.5+dfsg-1 / 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: 07780f081662b6aee2b279ff363d299297983e7518eed46feb21f85d07fbcefd

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

printf '%s  %s\n' '07780f081662b6aee2b279ff363d299297983e7518eed46feb21f85d07fbcefd' 'spades_4.0.0+really3.15.5+dfsg-1_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 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3

Повнота запису каталогу

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 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3. The cross-OS mapping is catalog-derived from the source-reported homepage; it does not establish authorship or publisher identity

Джерела та походження

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 13 (Trixie) main amd64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3
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/trixie/InRelease
Signed-object SHA-256
98b25b5cd185c59d34aa6e4c3e9b5b8f01bbe9d104fe2dcfbcd30dc0a14a59ed
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: 3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3
Observed SHA-256: 3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3
Result: match verified