LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
admin/requirements.txt
aviary/__init__.py
aviary/aviary.py
aviary/pixi.lock
aviary/pixi.toml
aviary/config/__init__.py
aviary/config/config.py
aviary/envs/__init__.py
aviary/envs/webpage.yaml
aviary/modules/Snakefile
aviary/modules/__init__.py
aviary/modules/common.py
aviary/modules/processor.py
aviary/modules/template_config.yaml
aviary/modules/annotation/__init__.py
aviary/modules/annotation/annotation.smk
aviary/modules/annotation/scripts/__init__.py
aviary/modules/assembly/__init__.py
aviary/modules/assembly/assembly.smk
aviary/modules/assembly/isolate.smk
aviary/modules/assembly/scripts/__init__.py
aviary/modules/assembly/scripts/assemble_pools.py
aviary/modules/assembly/scripts/assemble_short_reads.py
aviary/modules/assembly/scripts/combine_assemblies.py
aviary/modules/assembly/scripts/filter_illumina_assembly.py
aviary/modules/assembly/scripts/generate_pilon_sort.py
aviary/modules/assembly/scripts/get_binned_reads.py
aviary/modules/assembly/scripts/polish.py
aviary/modules/assembly/scripts/pool_reads.py
aviary/modules/assembly/scripts/run_flye.py
aviary/modules/assembly/scripts/run_myloasm.py
aviary/modules/assembly/scripts/spades_assembly.py
aviary/modules/binning/__init__.py
aviary/modules/binning/binning.smk
aviary/modules/binning/scripts/__init__.py
aviary/modules/binning/scripts/convert_metabuli.py
aviary/modules/binning/scripts/das_tool.py
aviary/modules/binning/scripts/filter_bins_for_quality.py
aviary/modules/binning/scripts/finalise_recovery.py
aviary/modules/binning/scripts/finalise_stats.py
aviary/modules/binning/scripts/get_abundances.py
aviary/modules/binning/scripts/get_coverage.py
aviary/modules/binning/scripts/make_long_cov.py
aviary/modules/binning/scripts/prepare_rosella_input.py
aviary/modules/binning/scripts/rosella_refine.py
aviary/modules/binning/scripts/run_checkm.py
aviary/modules/binning/scripts/write_vamb_bins.py
aviary/modules/cluster/__init__.py
aviary/modules/cluster/clustering.smk
aviary/modules/cluster/scripts/__init__.py
aviary/modules/quality_control/__init__.py
aviary/modules/quality_control/qc.smk
aviary/modules/quality_control/scripts/__init__.py
aviary/modules/quality_control/scripts/filter_read_list.py
aviary/modules/quality_control/scripts/fraction_recovered.py
aviary/modules/quality_control/scripts/qc_long_reads.py
aviary/modules/quality_control/scripts/qc_short_reads.py
aviary/modules/quality_control/scripts/run_rastqc.py
aviary/scripts/__init__.py
aviary/scripts/run_busco.py
aviary/scripts/run_virfinder.R
aviary/scripts/singlem_appraise.py
aviary/scripts/singlem_reads.py
aviary/web/__init__.py
aviary/web/generate_report.py
aviary/web/server.py
aviary/web/singlem_scanner.py
aviary/web/utils.py
aviary_genome.egg-info/PKG-INFO
aviary_genome.egg-info/SOURCES.txt
aviary_genome.egg-info/dependency_links.txt
aviary_genome.egg-info/entry_points.txt
aviary_genome.egg-info/not-zip-safe
aviary_genome.egg-info/requires.txt
aviary_genome.egg-info/top_level.txt
test/test_annotate.py
test/test_assemble.py
test/test_build.py
test/test_complete.py
test/test_convert_metabuli.py
test/test_integration.py
test/test_recover.py
test/test_run_checkm.py
test/test_run_workflow_errors.py