python-scripts/concat-gfas
site-packages/hybracter-0.12.0.dist-info/INSTALLER
site-packages/hybracter-0.12.0.dist-info/METADATA
site-packages/hybracter-0.12.0.dist-info/RECORD
site-packages/hybracter-0.12.0.dist-info/REQUESTED
site-packages/hybracter-0.12.0.dist-info/WHEEL
site-packages/hybracter-0.12.0.dist-info/direct_url.json
site-packages/hybracter-0.12.0.dist-info/entry_points.txt
site-packages/hybracter-0.12.0.dist-info/licenses/LICENSE
site-packages/hybracter-0.12.0.dist-info/top_level.txt
site-packages/hybracter/__init__.py
site-packages/hybracter/__main__.py
site-packages/hybracter/concat_GFAs_hybracter.py
site-packages/hybracter/config/config.yaml
site-packages/hybracter/contaminant_genomes/lambda.fasta
site-packages/hybracter/hybracter.CITATION
site-packages/hybracter/hybracter.LICENSE
site-packages/hybracter/hybracter.VERSION
site-packages/hybracter/test_data/Fastqs/C222_plasmid.fasta
site-packages/hybracter/test_data/Fastqs/assembly.fasta
site-packages/hybracter/test_data/Fastqs/generating_simulated_reads.sh
site-packages/hybracter/test_data/Fastqs/test_long_reads.fastq
site-packages/hybracter/test_data/Fastqs/test_long_reads.fastq.gz
site-packages/hybracter/test_data/Fastqs/test_long_reads_subsampled.fastq.gz
site-packages/hybracter/test_data/Fastqs/test_short_reads_R1.fastq.gz
site-packages/hybracter/test_data/Fastqs/test_short_reads_R2.fastq.gz
site-packages/hybracter/test_data/Fastqs/test_short_reads_low_depth_R1.fastq
site-packages/hybracter/test_data/Fastqs/test_short_reads_low_depth_R1.fastq.gz
site-packages/hybracter/test_data/Fastqs/test_short_reads_low_depth_R2.fastq
site-packages/hybracter/test_data/Fastqs/test_short_reads_low_depth_R2.fastq.gz
site-packages/hybracter/test_data/Fastqs/test_short_reads_ultra_low_depth_R1.fastq.gz
site-packages/hybracter/test_data/Fastqs/test_short_reads_ultra_low_depth_R2.fastq.gz
site-packages/hybracter/test_data/Plassembler_DB_Test/plsdb.fasta
site-packages/hybracter/test_data/Plassembler_DB_Test/plsdb_2023_11_03_v2.msh
site-packages/hybracter/test_data/Plassembler_DB_Test/plsdb_2023_11_03_v2.tsv
site-packages/hybracter/test_data/dnaapler_custom_db/all.faa
site-packages/hybracter/test_data/test_hybrid_input.csv
site-packages/hybracter/test_data/test_hybrid_input_auto.csv
site-packages/hybracter/test_data/test_hybrid_input_datadir.csv
site-packages/hybracter/test_data/test_hybrid_input_low_illumina_coverage.csv
site-packages/hybracter/test_data/test_hybrid_input_not_gzipped.csv
site-packages/hybracter/test_data/test_hybrid_input_ultra_low_illumina_coverage.csv
site-packages/hybracter/test_data/test_long_input.csv
site-packages/hybracter/test_data/test_long_input_auto.csv
site-packages/hybracter/test_data/test_long_input_datadir.csv
site-packages/hybracter/util.py
site-packages/hybracter/workflow/envs/ale.yaml
site-packages/hybracter/workflow/envs/bwa.yaml
site-packages/hybracter/workflow/envs/contaminants.yaml
site-packages/hybracter/workflow/envs/coverage.yaml
site-packages/hybracter/workflow/envs/dnaapler.yaml
site-packages/hybracter/workflow/envs/fastp.yaml
site-packages/hybracter/workflow/envs/filtlong.yaml
site-packages/hybracter/workflow/envs/flye.yaml
site-packages/hybracter/workflow/envs/kmc.yaml
site-packages/hybracter/workflow/envs/lrge.yaml
site-packages/hybracter/workflow/envs/medaka.yaml
site-packages/hybracter/workflow/envs/medaka_mac.yaml
site-packages/hybracter/workflow/envs/plassembler.yaml
site-packages/hybracter/workflow/envs/polypolish.yaml
site-packages/hybracter/workflow/envs/porechop_abi.yaml
site-packages/hybracter/workflow/envs/pypolca.yaml
site-packages/hybracter/workflow/envs/pyrodigal.yaml
site-packages/hybracter/workflow/envs/scripts.yaml
site-packages/hybracter/workflow/envs/seqkit.yaml
site-packages/hybracter/workflow/hybrid.smk
site-packages/hybracter/workflow/install.smk
site-packages/hybracter/workflow/long.smk
site-packages/hybracter/workflow/rules/assembly/assemble.smk
site-packages/hybracter/workflow/rules/assembly/plassembler.smk
site-packages/hybracter/workflow/rules/assembly/plassembler_long.smk
site-packages/hybracter/workflow/rules/assess/assess_complete.smk
site-packages/hybracter/workflow/rules/assess/assess_complete_no_medaka.smk
site-packages/hybracter/workflow/rules/assess/assess_incomplete.smk
site-packages/hybracter/workflow/rules/assess/assess_incomplete_no_medaka.smk
site-packages/hybracter/workflow/rules/completeness/aggregate.smk
site-packages/hybracter/workflow/rules/completeness/aggregate_long.smk
site-packages/hybracter/workflow/rules/download/download_medaka_models.smk
site-packages/hybracter/workflow/rules/download/download_plassembler_db.smk
site-packages/hybracter/workflow/rules/finalise/select_best_assembly.smk
site-packages/hybracter/workflow/rules/finalise/select_best_assembly_long.smk
site-packages/hybracter/workflow/rules/finalise/select_best_assembly_long_no_medaka.smk
site-packages/hybracter/workflow/rules/finalise/select_best_assembly_no_medaka.smk
site-packages/hybracter/workflow/rules/polishing/long_read_polish.smk
site-packages/hybracter/workflow/rules/polishing/long_read_polish_incomplete.smk
site-packages/hybracter/workflow/rules/polishing/short_read_polish.smk
site-packages/hybracter/workflow/rules/polishing/short_read_polish_incomplete.smk
site-packages/hybracter/workflow/rules/polishing/short_read_polish_incomplete_no_medaka.smk
site-packages/hybracter/workflow/rules/polishing/short_read_polish_no_medaka.smk
site-packages/hybracter/workflow/rules/polishing/short_read_pypolca.smk
site-packages/hybracter/workflow/rules/polishing/short_read_pypolca_no_medaka.smk
site-packages/hybracter/workflow/rules/preflight/directories.smk
site-packages/hybracter/workflow/rules/preflight/functions.smk
site-packages/hybracter/workflow/rules/preflight/samples.smk
site-packages/hybracter/workflow/rules/preflight/targets_download.smk
site-packages/hybracter/workflow/rules/preflight/targets_hybrid.smk
site-packages/hybracter/workflow/rules/preflight/targets_long.smk
site-packages/hybracter/workflow/rules/processing/combine_plassembler_info.smk
site-packages/hybracter/workflow/rules/processing/coverage.smk
site-packages/hybracter/workflow/rules/processing/estimate_chromosome.smk
site-packages/hybracter/workflow/rules/processing/extract_fastas.smk
site-packages/hybracter/workflow/rules/processing/qc.smk
site-packages/hybracter/workflow/rules/processing/remove_contaminants_qc.smk
site-packages/hybracter/workflow/rules/processing/skip_qc.smk
site-packages/hybracter/workflow/rules/reorientation/dnaapler.smk
site-packages/hybracter/workflow/rules/reorientation/dnaapler_custom.smk
site-packages/hybracter/workflow/rules/reorientation/dnaapler_custom_no_medaka.smk
site-packages/hybracter/workflow/rules/reorientation/dnaapler_no_medaka.smk
site-packages/hybracter/workflow/scripts/add_sample_plassembler.py
site-packages/hybracter/workflow/scripts/assess_plassembler_long_complete.py
site-packages/hybracter/workflow/scripts/check_completeness.py
site-packages/hybracter/workflow/scripts/combine_plassembler_info.py
site-packages/hybracter/workflow/scripts/compare_assemblies.py
site-packages/hybracter/workflow/scripts/create_final_hybracter_summary.py
site-packages/hybracter/workflow/scripts/extract_chromosome.py
site-packages/hybracter/workflow/scripts/extract_incomplete.py
site-packages/hybracter/workflow/scripts/extract_plasmids.py
site-packages/hybracter/workflow/scripts/lr_coverage.py
site-packages/hybracter/workflow/scripts/no_medaka/assess_plassembler_long_complete.py
site-packages/hybracter/workflow/scripts/no_medaka/select_best_chromosome_assembly_complete.py
site-packages/hybracter/workflow/scripts/no_medaka/select_best_chromosome_assembly_incomplete.py
site-packages/hybracter/workflow/scripts/no_medaka/select_best_chromosome_assembly_long_complete.py
site-packages/hybracter/workflow/scripts/no_medaka/select_best_chromosome_assembly_long_incomplete.py
site-packages/hybracter/workflow/scripts/pyrodigal_helpers.py
site-packages/hybracter/workflow/scripts/select_best_chromosome_assembly_complete.py
site-packages/hybracter/workflow/scripts/select_best_chromosome_assembly_incomplete.py
site-packages/hybracter/workflow/scripts/select_best_chromosome_assembly_long_complete.py
site-packages/hybracter/workflow/scripts/select_best_chromosome_assembly_long_incomplete.py
site-packages/hybracter/workflow/scripts/sr_coverage.py
site-packages/hybracter/workflow/scripts/write_chrom_size.py
site-packages/hybracter/workflow/test_hybrid.smk
site-packages/hybracter/workflow/test_long.smk
