discosnp (1:2.6.2-5)

Details

Core information at a glance

Distribution
ubuntu
Origin
ubuntu-stonking
Repository
https://nl.archive.ubuntu.com/ubuntu
Codename
stonking
Component
universe
Source
none
Architecture
amd64v3
Section
universe/science
Priority
optional
Maintainer
Ubuntu Developers <[email protected]>

Size & integrity

Byte sizes and integrity verification

Installed size
2.7 kB
Size expected
1.5 MB
Size actual
1.5 MB
Size match

Dependencies

Required package dependencies

  • libc6 (>= 2.38)
  • libgatbcore3 (>= 1.4.2)
  • libgcc-s1 (>= 3.3.1)
  • libhdf5-310 (>= 1.14.3)
  • libstdc++6 (>= 14)
  • zlib1g (>= 1:1.2.6)
  • python3:any
  • python3
  • gatb-core

Suggested packages

Recommended additional packages

  • None

Description

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

Homepage Download .deb

Tags

Package classification tags

None

Checksums

Hash values and integrity verification status

TypeActualMatch
MD51f630d6f…36e84d16
SHA-159186e66…da792064
SHA-256ea01f149…fbe808de
SHA-512657ed96e…7fa54b8e

Contents

Files and directories included

.
usr
usr/bin
usr/bin/create_coverage_h5_file
usr/bin/kissnp2
usr/bin/kissreads2
usr/bin/run_discoSnp++.sh
usr/bin/run_discoSnp++_ML.sh
usr/lib
usr/lib/discosnp
usr/lib/discosnp/bin
usr/lib/discosnp/bin/quick_hierarchical_clustering
usr/lib/discosnp/bin/read_file_names
usr/share
usr/share/discosnp
usr/share/discosnp/discoSnpRAD
usr/share/discosnp/discoSnpRAD/COOKBOOK.md
usr/share/discosnp/discoSnpRAD/README.md
usr/share/discosnp/discoSnpRAD/clustering_scripts
usr/share/discosnp/discoSnpRAD/clustering_scripts/README.md
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/post-processing_scripts
usr/share/discosnp/discoSnpRAD/post-processing_scripts/1SNP_per_cluster.py
usr/share/discosnp/discoSnpRAD/post-processing_scripts/README.md
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/vcf2structure.sh
usr/share/discosnp/discoSnpRAD/run_discoSnpRad.sh
usr/share/discosnp/scripts
usr/share/discosnp/scripts/ClassVCF_creator.py
usr/share/discosnp/scripts/VCF_creator.py
usr/share/discosnp/scripts/clusters_and_fasta_to_fasta.py_DEPRECATED
usr/share/discosnp/scripts/create_IGV_compatible_VCF.sh
usr/share/discosnp/scripts/create_filtered_vcf.py
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_K2000.py
usr/share/discosnp/scripts/format_phased_for_clustering.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
usr/share/discosnp/scripts/k3000/From phased facts to gfa graph.pdf
usr/share/discosnp/scripts/k3000/K3000.py
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_working_zone.py
usr/share/discosnp/scripts/k3000/K3000_working_zone_no_redundant_edges.py
usr/share/discosnp/scripts/k3000/Snakefile
usr/share/discosnp/scripts/k3000/compute_pi.py
usr/share/discosnp/scripts/k3000/extract_DP_from_vcf.py
usr/share/discosnp/scripts/k3000/negative_binomial.py
usr/share/discosnp/scripts/k3000/run_K3000.sh
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
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
usr/share/discosnp/scripts/simulations/README.md
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/targeted_mut_fasta_corrected.py
usr/share/discosnp/scripts/split_multiple_snps.py
usr/share/discosnp/scripts/validation_scripts
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_formatting_functions.py
usr/share/discosnp/scripts/zero2one.py
usr/share/doc
usr/share/doc/discosnp
usr/share/doc/discosnp/README.Debian
usr/share/doc/discosnp/README.md.gz
usr/share/doc/discosnp/README.test
usr/share/doc/discosnp/changelog.Debian.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/run-unit-test
usr/share/doc/discosnp/test
usr/share/doc/discosnp/test/fof.txt
usr/share/doc/discosnp/test/large_test
usr/share/doc/discosnp/test/large_test/fof_rad.txt
usr/share/doc/discosnp/test/large_test/fof_rad_indel.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
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/ref_version.txt
usr/share/doc/discosnp/test/reference_genome.fa
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
usr/share/lintian/overrides
usr/share/lintian/overrides/discosnp
usr/share/man
usr/share/man/man1
usr/share/man/man1/kissnp2.1.gz
usr/share/man/man1/kissreads2.1.gz
usr/share/man/man1/run_discoSnp++.sh.1.gz
usr/share/man/man1/run_discoSnpRad.sh.1.gz
usr/share/python3
usr/share/python3/runtime.d
usr/share/python3/runtime.d/discosnp.rtupdate