Linux workstation

Debian 12 (Bookworm) native package

discosnp

discovering Single Nucleotide Polymorphism from raw set(s) of reads

Packages / Debian 12 (Bookworm) / science / discosnp

Package: discosnp (1:2.6.2-2)

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [colibread.inria.fr]

discovering Single Nucleotide Polymorphism from raw set(s) of reads

Other Packages Related to discosnp:

  • dep: [libc6] (>= 2.34)

    GNU C Library: Shared libraries

  • dep: [libgatbcore3] (>= 1.4.2)

    dynamic library of the Genome Analysis Toolbox

  • dep: [libgcc-s1] (>= 3.0)

    GCC support library

  • dep: [libhdf5-103-1]

    HDF5 C runtime files - serial version

  • dep: [libstdc++6] (>= 11)

    GNU Standard C++ Library v3

  • dep: [zlib1g] (>= 1:1.2.6)

    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: [gatb-core]

    Genome Analysis Toolbox with de-Bruijn graph

Download discosnp

ArchitecturePackage SizeInstalled SizeFiles
amd641.4 MiB2.8 MiB[list of files]
arm641.4 MiB3.0 MiB[list of files]

Package file paths (119)

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/create_coverage_h5_file
  • /usr/bin/kissnp2
  • /usr/bin/kissreads2
  • /usr/bin/run_discoSnp++_ML.sh
  • /usr/bin/run_discoSnp++.sh
  • /usr/lib/discosnp/bin/quick_hierarchical_clustering
  • /usr/lib/discosnp/bin/read_file_names
  • /usr/share/discosnp/discoSnpRAD/clustering_scripts/discoRAD_clustering.sh
  • /usr/share/discosnp/discoSnpRAD/clustering_scripts/fasta_and_cluster_to_filtered_vcf.py
  • /usr/share/discosnp/discoSnpRAD/clustering_scripts/from_SRC_to_edges.py
  • /usr/share/discosnp/discoSnpRAD/clustering_scripts/README.md
  • /usr/share/discosnp/discoSnpRAD/COOKBOOK.md
  • /usr/share/discosnp/discoSnpRAD/post-processing_scripts/1SNP_per_cluster.py
  • /usr/share/discosnp/discoSnpRAD/post-processing_scripts/add_cluster_info_to_mapped_vcf.py
  • /usr/share/discosnp/discoSnpRAD/post-processing_scripts/filter_by_cluster_size_and_rank.py
  • /usr/share/discosnp/discoSnpRAD/post-processing_scripts/filter_paralogs.py
  • /usr/share/discosnp/discoSnpRAD/post-processing_scripts/filter_vcf_by_indiv_cov_max_missing_and_maf.py
  • /usr/share/discosnp/discoSnpRAD/post-processing_scripts/README.md
  • /usr/share/discosnp/discoSnpRAD/post-processing_scripts/vcf2structure.sh
  • /usr/share/discosnp/discoSnpRAD/README.md
  • /usr/share/discosnp/discoSnpRAD/run_discoSnpRad.sh
  • /usr/share/discosnp/scripts/ClassVCF_creator.py
  • /usr/share/discosnp/scripts/clusters_and_fasta_to_fasta.py_DEPRECATED
  • /usr/share/discosnp/scripts/create_filtered_vcf.py
  • /usr/share/discosnp/scripts/create_IGV_compatible_VCF.sh
  • /usr/share/discosnp/scripts/discoSnp++_to_csv.py
  • /usr/share/discosnp/scripts/filterOnBestDP_multiple_variant_at_same_pos.py
  • /usr/share/discosnp/scripts/filter_out_using_MAF.py
  • /usr/share/discosnp/scripts/filter_out_using_ratio_of_covered_files.py
  • /usr/share/discosnp/scripts/format_phased_for_clustering.py
  • /usr/share/discosnp/scripts/format_phased_for_K2000.py
  • /usr/share/discosnp/scripts/format_phased_variants_for_haplotyping.py
  • /usr/share/discosnp/scripts/from_path_to_edges.py
  • /usr/share/discosnp/scripts/from_phased_alleles_to_clusters.sh
  • /usr/share/discosnp/scripts/functionObjectVCF_creator.py
  • /usr/share/discosnp/scripts/k3000/compute_pi.py
  • /usr/share/discosnp/scripts/k3000/extract_DP_from_vcf.py
  • /usr/share/discosnp/scripts/k3000/From phased facts to gfa graph.pdf
  • /usr/share/discosnp/scripts/k3000/K3000_common.py
  • /usr/share/discosnp/scripts/k3000/K3000_enhance_gfa.py
  • /usr/share/discosnp/scripts/k3000/K3000_fact_haplotypes_to_localized_variant_ids.py
  • /usr/share/discosnp/scripts/k3000/K3000_facts_to_fa.py
  • /usr/share/discosnp/scripts/k3000/K3000_facts_to_gfa.py
  • /usr/share/discosnp/scripts/k3000/K3000_filter_badly_overlapping_variants.py
  • /usr/share/discosnp/scripts/k3000/K3000_find_unitig_connected_pairs_of_facts.py
  • /usr/share/discosnp/scripts/k3000/K3000_gfa_post_treatment.py
  • /usr/share/discosnp/scripts/k3000/K3000_gfa_to_dat.py
  • /usr/share/discosnp/scripts/k3000/K3000_gfa_to_fa.py
  • /usr/share/discosnp/scripts/k3000/K3000_msr_to_gfa.py
  • /usr/share/discosnp/scripts/k3000/K3000_node_ids_to_node_sequences.py
  • /usr/share/discosnp/scripts/k3000/K3000_paths_to_fa.py
  • /usr/share/discosnp/scripts/k3000/K3000_phased_paths_to_fa.py
  • /usr/share/discosnp/scripts/k3000/K3000.py
  • /usr/share/discosnp/scripts/k3000/K3000_working_zone_no_redundant_edges.py
  • /usr/share/discosnp/scripts/k3000/K3000_working_zone.py
  • /usr/share/discosnp/scripts/k3000/negative_binomial.py
  • /usr/share/discosnp/scripts/k3000/run_K3000.sh
  • /usr/share/discosnp/scripts/k3000/Snakefile
  • /usr/share/discosnp/scripts/k3000/sorted_list.py
  • /usr/share/discosnp/scripts/k3000/stats.py
  • /usr/share/discosnp/scripts/keep_extensions_disco_file.py
  • /usr/share/discosnp/scripts/phasing/phased_variants_to_graph_deprecated.py
  • /usr/share/discosnp/scripts/redundancy_removal_discosnp.py
  • /usr/share/discosnp/scripts/remove_extensions_disco_file.py
  • /usr/share/discosnp/scripts/remove_non_biallelic.py
  • /usr/share/discosnp/scripts/remove_non_covered_genotypes.py
  • /usr/share/discosnp/scripts/run_VCF_creator.sh
  • /usr/share/discosnp/scripts/simulations/ill100v4.bad.qual
  • /usr/share/discosnp/scripts/simulations/ill100v4.good.qual
  • /usr/share/discosnp/scripts/simulations/multiple_samples_simulator.sh
  • /usr/share/discosnp/scripts/simulations/random_mut_fasta.py
  • /usr/share/discosnp/scripts/simulations/README.md
  • /usr/share/discosnp/scripts/simulations/targeted_mut_fasta_corrected.py
  • /usr/share/discosnp/scripts/split_multiple_snps.py
  • /usr/share/discosnp/scripts/validation_scripts/compare_vcf_disco_pos_allele_only.py
  • /usr/share/discosnp/scripts/validation_scripts/eval_disco_one_snp_per_locus.py
  • /usr/share/discosnp/scripts/VCF_creator.py
  • /usr/share/discosnp/scripts/vcf_formatting_functions.py
  • /usr/share/discosnp/scripts/zero2one.py
  • /usr/share/doc/discosnp/changelog.Debian.gz
  • /usr/share/doc/discosnp/changelog.gz
  • /usr/share/doc/discosnp/copyright
  • /usr/share/doc/discosnp/discoSnp_user_guide.odt
  • /usr/share/doc/discosnp/discoSnp_user_guide.pdf.gz
  • /usr/share/doc/discosnp/discoSnp_user_guide.txt.gz
  • /usr/share/doc/discosnp/README.Debian
  • /usr/share/doc/discosnp/README.md.gz
  • /usr/share/doc/discosnp/README.test
  • /usr/share/doc/discosnp/run-unit-test
  • /usr/share/doc/discosnp/test/fof.txt
  • /usr/share/doc/discosnp/test/large_test/fof_rad_indel.txt
  • /usr/share/doc/discosnp/test/large_test/fof_rad.txt
  • /usr/share/doc/discosnp/test/large_test/generate_refs.sh
  • /usr/share/doc/discosnp/test/large_test/large_test.sh
  • /usr/share/doc/discosnp/test/large_test/local_large_test.sh.gz
  • /usr/share/doc/discosnp/test/large_test/rad_option_test/fof_rad.txt_radtest_k_31_c_auto_D_0_P_4_b_2_removemeplease
  • /usr/share/doc/discosnp/test/large_test/rad_option_test/loci_reads.gz
  • /usr/share/doc/discosnp/test/large_test/rad_option_test/loci_reads_one_indel.gz
  • /usr/share/doc/discosnp/test/large_test/rad_option_test/radref_k_31_c_auto_D_0_P_4_b_2_coherent.fa
  • /usr/share/doc/discosnp/test/reads_sequence1.fasta.gz
  • /usr/share/doc/discosnp/test/reads_sequence2.fasta.gz
  • /usr/share/doc/discosnp/test/ref_discoRes_k_31_c_3_D_100_P_1_b_0_coherent.fa.gz
  • /usr/share/doc/discosnp/test/ref_discoRes_k_31_c_3_D_100_P_1_b_0_coherent.vcf
  • /usr/share/doc/discosnp/test/ref_discoRes_k_31_c_3_D_100_P_3_b_0_coherent.fa.gz
  • /usr/share/doc/discosnp/test/ref_discoRes_k_31_c_3_D_100_P_3_b_0_coherent.vcf
  • /usr/share/doc/discosnp/test/ref_discoRes_k_31_c_auto_D_100_P_1_b_0_coherent.fa.gz
  • /usr/share/doc/discosnp/test/ref_discoRes_k_31_c_auto_D_100_P_1_b_0_coherent.vcf
  • /usr/share/doc/discosnp/test/reference_genome.fa
  • /usr/share/doc/discosnp/test/ref_version.txt
  • /usr/share/doc/discosnp/test/simple_test.sh
  • /usr/share/doc/discosnp/vcf_creator_user_guide.odt
  • /usr/share/doc/discosnp/vcf_creator_user_guide.pdf.gz
  • /usr/share/doc/discosnp/vcf_creator_user_guide.txt.gz
  • /usr/share/lintian/overrides/discosnp
  • /usr/share/man/man1/kissnp2.1.gz
  • /usr/share/man/man1/kissreads2.1.gz
  • /usr/share/man/man1/run_discoSnpRad.sh.1.gz
  • /usr/share/man/man1/run_discoSnp++.sh.1.gz
  • /usr/share/python3/runtime.d/discosnp.rtupdate

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 discosnp

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
1:2.6.2-2bookworm / mainamd64Debian 12 · main · amd641.4 MiB2.8 MiBpool/main/d/discosnp/discosnp_2.6.2-2_amd64.deb
1:2.6.2-2bookworm / mainarm64Debian 12 · main · arm641.4 MiB3.0 MiBpool/main/d/discosnp/discosnp_2.6.2-2_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.

1:2.6.2-2 / 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: a55cb4a88c1d0af3d717a9e7d8d95fbd3ea6b3ca639d50e30e796f126f90c546

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

printf '%s %s\n' 'a55cb4a88c1d0af3d717a9e7d8d95fbd3ea6b3ca639d50e30e796f126f90c546' 'discosnp_2.6.2-2_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

1:2.6.2-2 / 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: dfc78fb0c170ac3bc1595e38cef07339841146bee12861d299d7121337db039e

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

printf '%s %s\n' 'dfc78fb0c170ac3bc1595e38cef07339841146bee12861d299d7121337db039e' 'discosnp_2.6.2-2_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

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