bin/.spades-post-link.sh
bin/coronaspades.py
bin/metaplasmidspades.py
bin/metaspades.py
bin/metaviralspades.py
bin/plasmidspades.py
bin/rnaspades.py
bin/rnaviralspades.py
bin/spades-bwa
bin/spades-convert-bin-to-fasta
bin/spades-core
bin/spades-corrector-core
bin/spades-gbuilder
bin/spades-gfa-split
bin/spades-gmapper
bin/spades-gsimplifier
bin/spades-hammer
bin/spades-ionhammer
bin/spades-kmer-estimating
bin/spades-kmercount
bin/spades-read-filter
bin/spades.py
bin/spades_init.py
share/spades/GPLv2.txt
share/spades/LICENSE
share/spades/README.md
share/spades/VERSION
share/spades/biosynthetic_spades_hmms/AMP.hmm.gz
share/spades/biosynthetic_spades_hmms/AT.hmm.gz
share/spades/biosynthetic_spades_hmms/CStart.hmm.gz
share/spades/biosynthetic_spades_hmms/KR.hmm.gz
share/spades/biosynthetic_spades_hmms/KS.hmm.gz
share/spades/biosynthetic_spades_hmms/TE.hmm.gz
share/spades/configs/corrector/corrector.info
share/spades/configs/debruijn/careful_mda_mode.info
share/spades/configs/debruijn/careful_mode.info
share/spades/configs/debruijn/config.info
share/spades/configs/debruijn/construction.info
share/spades/configs/debruijn/detail_info_printer.info
share/spades/configs/debruijn/distance_estimation.info
share/spades/configs/debruijn/hmm_mode.info
share/spades/configs/debruijn/isolate_mode.info
share/spades/configs/debruijn/large_genome_mode.info
share/spades/configs/debruijn/mda_mode.info
share/spades/configs/debruijn/meta_mode.info
share/spades/configs/debruijn/metaplasmid_mode.info
share/spades/configs/debruijn/metaviral_mode.info
share/spades/configs/debruijn/pe_params.info
share/spades/configs/debruijn/plasmid_mode.info
share/spades/configs/debruijn/rna_mode.info
share/spades/configs/debruijn/rnaviral_mode.info
share/spades/configs/debruijn/sewage_mode.info
share/spades/configs/debruijn/simplification.info
share/spades/configs/debruijn/toy.info
share/spades/configs/hammer/config.info
share/spades/configs/ionhammer/ionhammer.cfg
share/spades/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz
share/spades/coronaspades_hmms/Phan-CoV.hmm.gz
share/spades/joblib3/__init__.py
share/spades/joblib3/_compat.py
share/spades/joblib3/_memory_helpers.py
share/spades/joblib3/_multiprocessing_helpers.py
share/spades/joblib3/disk.py
share/spades/joblib3/format_stack.py
share/spades/joblib3/func_inspect.py
share/spades/joblib3/hashing.py
share/spades/joblib3/logger.py
share/spades/joblib3/memory.py
share/spades/joblib3/my_exceptions.py
share/spades/joblib3/numpy_pickle.py
share/spades/joblib3/parallel.py
share/spades/joblib3/pool.py
share/spades/joblib3/testing.py
share/spades/pyyaml3/__init__.py
share/spades/pyyaml3/composer.py
share/spades/pyyaml3/constructor.py
share/spades/pyyaml3/cyaml.py
share/spades/pyyaml3/dumper.py
share/spades/pyyaml3/emitter.py
share/spades/pyyaml3/error.py
share/spades/pyyaml3/events.py
share/spades/pyyaml3/loader.py
share/spades/pyyaml3/nodes.py
share/spades/pyyaml3/parser.py
share/spades/pyyaml3/reader.py
share/spades/pyyaml3/representer.py
share/spades/pyyaml3/resolver.py
share/spades/pyyaml3/scanner.py
share/spades/pyyaml3/serializer.py
share/spades/pyyaml3/tokens.py
share/spades/sewage/usher_barcodes.csv
share/spades/spades_pipeline/commands_parser.py
share/spades/spades_pipeline/common/SeqIO.py
share/spades/spades_pipeline/common/__init__.py
share/spades/spades_pipeline/common/alignment.py
share/spades/spades_pipeline/common/parallel_launcher.py
share/spades/spades_pipeline/common/sam_parser.py
share/spades/spades_pipeline/executors/executor_local.py
share/spades/spades_pipeline/executors/executor_save_yaml.py
share/spades/spades_pipeline/executors/executors.py
share/spades/spades_pipeline/options_parser.py
share/spades/spades_pipeline/options_storage.py
share/spades/spades_pipeline/process_cfg.py
share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py
share/spades/spades_pipeline/scripts/check_test_script.py
share/spades/spades_pipeline/scripts/compress_all.py
share/spades/spades_pipeline/scripts/copy_files.py
share/spades/spades_pipeline/scripts/correction_iteration_script.py
share/spades/spades_pipeline/scripts/plasmid_glue.py
share/spades/spades_pipeline/scripts/preprocess_contigs.py
share/spades/spades_pipeline/scripts/preprocess_interlaced_reads.py
share/spades/spades_pipeline/stages/__init__.py
share/spades/spades_pipeline/stages/before_start_stage.py
share/spades/spades_pipeline/stages/breaking_scaffolds_stage.py
share/spades/spades_pipeline/stages/check_test_stage.py
share/spades/spades_pipeline/stages/correction_stage.py
share/spades/spades_pipeline/stages/error_correction_stage.py
share/spades/spades_pipeline/stages/pipeline.py
share/spades/spades_pipeline/stages/preprocess_reads_stage.py
share/spades/spades_pipeline/stages/scaffold_correction_stage.py
share/spades/spades_pipeline/stages/spades_iteration_stage.py
share/spades/spades_pipeline/stages/spades_stage.py
share/spades/spades_pipeline/stages/stage.py
share/spades/spades_pipeline/stages/terminating_stage.py
share/spades/spades_pipeline/support.py
share/spades/test_dataset/ecoli_1K_1.fq.gz
share/spades/test_dataset/ecoli_1K_2.fq.gz
share/spades/test_dataset/genes_1K.gff
share/spades/test_dataset/genes_1K.txt
share/spades/test_dataset/operons_1K.gff
share/spades/test_dataset/operons_1K.txt
share/spades/test_dataset/reference_1K.fa.gz
share/spades/test_dataset_plasmid/pl1.fq.gz
share/spades/test_dataset_plasmid/pl2.fq.gz
