Package - spades

Package:  spades
apt-get install spades
Manuals in package:
Documentations in package:

Primary informations

Download package: http://deb.debian.org/debian/pool/main/s/spades/spades_4.0.0+really3.15.5+dfsg-1_amd64.deb (Size: 8.8MiB)

PropertyValue
Packagespades
Version4.0.0+really3.15.5+dfsg-1
Installed-Size39919
MaintainerDebian Med Packaging Team
Architectureamd64
Dependslibc6 (>= 2.38), libgcc-s1 (>= 4.0), libgomp1 (>= 6), libnlopt0 (>= 2.6.1), libssw0 (>= 1.1), libstdc++6 (>= 14), zlib1g (>= 1:1.2.3.3), python3:any, python3, python3-joblib, python3-packaging, python3-yaml, bwa, bamtools, samtools
Descriptiongenome assembler for single-cell and isolates data sets
Description-md5d8ff9082fb3dd433b6c561c43ac72ddb
Homepagehttps://github.com/ablab/spades
Tagbiology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, implemented-in::python, interface::commandline, role::program, scope::utility, works-with::biological-sequence, works-with::file
Sectionscience
Priorityoptional
Filenamepool/main/s/spades/spades_4.0.0+really3.15.5+dfsg-1_amd64.deb
Size9243416
MD5sum601d4238e864f7e12915d4ced9fdc2b1
SHA25607780f081662b6aee2b279ff363d299297983e7518eed46feb21f85d07fbcefd

Files in package

  • /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/VERSION
  • /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-ionhammer
  • /usr/libexec/spades/spades-kmer-estimating
  • /usr/libexec/spades/spades-kmercount
  • /usr/libexec/spades/spades-read-filter
  • /usr/libexec/spades/spades-truseq-scfcorrection
  • /usr/libexec/spades/spades.py
  • /usr/libexec/spades/spades_init.py
  • /usr/libexec/spades/spaligner
  • /usr/libexec/spades/truspades.py
  • /usr/share/doc/spades/NEWS.Debian.gz
  • /usr/share/doc/spades/README.md.gz
  • /usr/share/doc/spades/README.test
  • /usr/share/doc/spades/changelog.Debian.gz
  • /usr/share/doc/spades/changelog.gz
  • /usr/share/doc/spades/copyright
  • /usr/share/doc/spades/examples/configs/README
  • /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/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/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/VERSION
  • /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/SeqIO.py
  • /usr/share/spades/spades_pipeline/common/__init__.py
  • /usr/share/spades/spades_pipeline/common/alignment.py
  • /usr/share/spades/spades_pipeline/common/parallel_launcher.py
  • /usr/share/spades/spades_pipeline/common/sam_parser.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/__init__.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/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/__init__.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/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/reference_1K.fa.gz
  • /usr/share/spades/test_dataset_plasmid/pl1.fq.gz
  • /usr/share/spades/test_dataset_plasmid/pl2.fq.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/spaligner/spaligner_config.yaml