LICENSE
README.md
site-packages/aviary/__init__.py
site-packages/aviary/aviary.py
site-packages/aviary/config/__init__.py
site-packages/aviary/config/config.py
site-packages/aviary/envs/__init__.py
site-packages/aviary/envs/webpage.yaml
site-packages/aviary/modules/Snakefile
site-packages/aviary/modules/__init__.py
site-packages/aviary/modules/annotation/__init__.py
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site-packages/aviary/modules/assembly/__init__.py
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site-packages/aviary/modules/assembly/scripts/assemble_short_reads.py
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site-packages/aviary/modules/assembly/scripts/filter_illumina_assembly.py
site-packages/aviary/modules/assembly/scripts/generate_pilon_sort.py
site-packages/aviary/modules/assembly/scripts/get_binned_reads.py
site-packages/aviary/modules/assembly/scripts/polish.py
site-packages/aviary/modules/assembly/scripts/pool_reads.py
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site-packages/aviary/modules/assembly/scripts/run_myloasm.py
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site-packages/aviary/modules/binning/__init__.py
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site-packages/aviary/modules/binning/scripts/convert_metabuli.py
site-packages/aviary/modules/binning/scripts/das_tool.py
site-packages/aviary/modules/binning/scripts/filter_bins_for_quality.py
site-packages/aviary/modules/binning/scripts/finalise_recovery.py
site-packages/aviary/modules/binning/scripts/finalise_stats.py
site-packages/aviary/modules/binning/scripts/get_abundances.py
site-packages/aviary/modules/binning/scripts/get_coverage.py
site-packages/aviary/modules/binning/scripts/make_long_cov.py
site-packages/aviary/modules/binning/scripts/prepare_rosella_input.py
site-packages/aviary/modules/binning/scripts/rosella_refine.py
site-packages/aviary/modules/binning/scripts/run_checkm.py
site-packages/aviary/modules/binning/scripts/write_vamb_bins.py
site-packages/aviary/modules/cluster/__init__.py
site-packages/aviary/modules/cluster/clustering.smk
site-packages/aviary/modules/cluster/scripts/__init__.py
site-packages/aviary/modules/common.py
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site-packages/aviary/modules/quality_control/__init__.py
site-packages/aviary/modules/quality_control/qc.smk
site-packages/aviary/modules/quality_control/scripts/__init__.py
site-packages/aviary/modules/quality_control/scripts/filter_read_list.py
site-packages/aviary/modules/quality_control/scripts/fraction_recovered.py
site-packages/aviary/modules/quality_control/scripts/qc_long_reads.py
site-packages/aviary/modules/quality_control/scripts/qc_short_reads.py
site-packages/aviary/modules/quality_control/scripts/run_rastqc.py
site-packages/aviary/modules/template_config.yaml
site-packages/aviary/pixi.lock
site-packages/aviary/pixi.toml
site-packages/aviary/scripts/__init__.py
site-packages/aviary/scripts/run_busco.py
site-packages/aviary/scripts/run_virfinder.R
site-packages/aviary/scripts/singlem_appraise.py
site-packages/aviary/scripts/singlem_reads.py
site-packages/aviary/web/__init__.py
site-packages/aviary/web/generate_report.py
site-packages/aviary/web/server.py
site-packages/aviary/web/singlem_scanner.py
site-packages/aviary/web/utils.py
site-packages/aviary_genome-0.13.0.dist-info/INSTALLER
site-packages/aviary_genome-0.13.0.dist-info/METADATA
site-packages/aviary_genome-0.13.0.dist-info/RECORD
site-packages/aviary_genome-0.13.0.dist-info/REQUESTED
site-packages/aviary_genome-0.13.0.dist-info/WHEEL
site-packages/aviary_genome-0.13.0.dist-info/direct_url.json
site-packages/aviary_genome-0.13.0.dist-info/entry_points.txt
site-packages/aviary_genome-0.13.0.dist-info/licenses/LICENSE
site-packages/aviary_genome-0.13.0.dist-info/top_level.txt
