README.md
setup.py
aquila_stlfr.egg-info/PKG-INFO
aquila_stlfr.egg-info/SOURCES.txt
aquila_stlfr.egg-info/dependency_links.txt
aquila_stlfr.egg-info/entry_points.txt
aquila_stlfr.egg-info/not-zip-safe
aquila_stlfr.egg-info/top_level.txt
bin/Aquila_stLFR_Contigs_WGS.py
bin/Aquila_stLFR_assembly_based_variants_call.py
bin/Aquila_stLFR_clean.py
bin/Aquila_stLFR_fastq_preprocess.py
bin/Aquila_stLFR_phasing_all_variants.py
bin/Aquila_stLFR_step1.py
bin/Aquila_stLFR_step2.py
bin/Aquila_step0_sortbam_hybrid.py
bin/Aquila_step1_hybrid.py
bin/Assign_phase_block_v3.py
bin/Assign_phase_block_v4.py
bin/Concatenate_contigs_all_v4_extend_for_HCbk.py
bin/Concatenate_contigs_from_microcontigs.py
bin/Cut_phaseblock_for_phased_h5_v4.0_highconf_v2.py
bin/Extract_DEL_allregions.py
bin/Extract_INS_allregions.py
bin/Extract_SNV_info_from_contigs_forcontiginfo_forall.py
bin/Extract_SV_info_from_contigs_use_overlap_for_del_forcontiginfo.py
bin/Extract_SV_info_from_contigs_use_shift_for_ins2_forcontiginfo.py
bin/Extract_qname_from_phased_molecule_cut_phase_blocks_v3.py
bin/Extract_qname_from_phased_molecule_cut_phase_blocks_v3_hybrid.py
bin/Generate_highconf_cut_profile_v2.py
bin/Make_supercontig_based_on_HCbk_from_sam_v5.py
bin/Merge_reads_for_PB_of_merged_libs_v2.py
bin/Molecule_phase_alg2_withProbModel_v3_MT2.py
bin/Molecule_phase_alg2_withProbModel_v3_MT2_hybrid.py
bin/Read_fastqs_from_sortedbam_v2.py
bin/Run_all_chunks.py
bin/Run_extract_reads_for_smallchunks_all_lessmem.py
bin/Run_extract_reads_for_smallchunks_all_lessmem_hybrid.py
bin/Run_h5_all_multithreads.py
bin/Run_microcontigs_all.py
bin/Run_phase_alg_multithreads2.py
bin/Run_phase_alg_multithreads2_hybrid.py
bin/Run_spades_final_MT_2_all_noec_deltemp.py
bin/Split_barcoded_fastq_by_chr_all_by_smallchunks.py
bin/__init__.py
bin/SPAdes-3.13.0-Linux/bin/metaspades.py
bin/SPAdes-3.13.0-Linux/bin/plasmidspades.py
bin/SPAdes-3.13.0-Linux/bin/rnaspades.py
bin/SPAdes-3.13.0-Linux/bin/spades-bwa
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bin/SPAdes-3.13.0-Linux/bin/spades-gbuilder
bin/SPAdes-3.13.0-Linux/bin/spades-gmapper
bin/SPAdes-3.13.0-Linux/bin/spades-hammer
bin/SPAdes-3.13.0-Linux/bin/spades-ionhammer
bin/SPAdes-3.13.0-Linux/bin/spades-kmercount
bin/SPAdes-3.13.0-Linux/bin/spades-truseq-scfcorrection
bin/SPAdes-3.13.0-Linux/bin/spades.py
bin/SPAdes-3.13.0-Linux/bin/spades_init.py
bin/SPAdes-3.13.0-Linux/bin/truspades.py
bin/SPAdes-3.13.0-Linux/share/spades/GPLv2.txt
bin/SPAdes-3.13.0-Linux/share/spades/LICENSE
bin/SPAdes-3.13.0-Linux/share/spades/README.md
bin/SPAdes-3.13.0-Linux/share/spades/VERSION
bin/SPAdes-3.13.0-Linux/share/spades/manual.html
bin/SPAdes-3.13.0-Linux/share/spades/rnaspades_manual.html
bin/SPAdes-3.13.0-Linux/share/spades/truspades_manual.html
bin/SPAdes-3.13.0-Linux/share/spades/configs/corrector/corrector.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/careful_mda_mode.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/careful_mode.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/config.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/construction.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/detail_info_printer.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/distance_estimation.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/large_genome_mode.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/mda_mode.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/meta_mode.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/moleculo_mode.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/pe_params.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/plasmid_mode.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/rna_fast_mode.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/rna_mode.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/simplification.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/toy.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/debruijn/tsa.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/hammer/config.info
bin/SPAdes-3.13.0-Linux/share/spades/configs/ionhammer/ionhammer.cfg
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bin/SPAdes-3.13.0-Linux/share/spades/joblib2/testing.py
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bin/SPAdes-3.13.0-Linux/share/spades/joblib3/_compat.py
bin/SPAdes-3.13.0-Linux/share/spades/joblib3/_memory_helpers.py
bin/SPAdes-3.13.0-Linux/share/spades/joblib3/_multiprocessing_helpers.py
bin/SPAdes-3.13.0-Linux/share/spades/joblib3/disk.py
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bin/SPAdes-3.13.0-Linux/share/spades/joblib3/func_inspect.py
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bin/SPAdes-3.13.0-Linux/share/spades/joblib3/logger.py
bin/SPAdes-3.13.0-Linux/share/spades/joblib3/memory.py
bin/SPAdes-3.13.0-Linux/share/spades/joblib3/my_exceptions.py
bin/SPAdes-3.13.0-Linux/share/spades/joblib3/numpy_pickle.py
bin/SPAdes-3.13.0-Linux/share/spades/joblib3/parallel.py
bin/SPAdes-3.13.0-Linux/share/spades/joblib3/pool.py
bin/SPAdes-3.13.0-Linux/share/spades/joblib3/testing.py
bin/SPAdes-3.13.0-Linux/share/spades/pyyaml2/__init__.py
bin/SPAdes-3.13.0-Linux/share/spades/pyyaml2/composer.py
bin/SPAdes-3.13.0-Linux/share/spades/pyyaml2/constructor.py
bin/SPAdes-3.13.0-Linux/share/spades/pyyaml2/cyaml.py
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bin/SPAdes-3.13.0-Linux/share/spades/pyyaml3/tokens.py
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bin/SPAdes-3.13.0-Linux/share/spades/spades_pipeline/hammer_logic.py
bin/SPAdes-3.13.0-Linux/share/spades/spades_pipeline/lucigen_nxmate.py
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bin/SPAdes-3.13.0-Linux/share/spades/spades_pipeline/common/SeqIO.py
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bin/SPAdes-3.13.0-Linux/share/spades/spades_pipeline/common/alignment.py
bin/SPAdes-3.13.0-Linux/share/spades/spades_pipeline/common/parallel_launcher.py
bin/SPAdes-3.13.0-Linux/share/spades/spades_pipeline/common/sam_parser.py
bin/SPAdes-3.13.0-Linux/share/spades/spades_pipeline/truspades/barcode_extraction.py
bin/SPAdes-3.13.0-Linux/share/spades/spades_pipeline/truspades/break_by_coverage.py
bin/SPAdes-3.13.0-Linux/share/spades/spades_pipeline/truspades/generate_quality.py
bin/SPAdes-3.13.0-Linux/share/spades/spades_pipeline/truspades/id_generation.py
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bin/SPAdes-3.13.0-Linux/share/spades/spades_pipeline/truspades/moleculo_filter_contigs.py
bin/SPAdes-3.13.0-Linux/share/spades/spades_pipeline/truspades/moleculo_postprocessing.py
bin/SPAdes-3.13.0-Linux/share/spades/spades_pipeline/truspades/reference_construction.py
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