LICENSE
README.md
setup.py
aviary/__init__.py
aviary/aviary.py
aviary/config/__init__.py
aviary/config/config.py
aviary/modules/__init__.py
aviary/modules/processor.py
aviary/modules/annotation/__init__.py
aviary/modules/annotation/scripts/__init__.py
aviary/modules/assembly/__init__.py
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/filter_illumina_reference.py
aviary/modules/assembly/scripts/filter_read_list.py
aviary/modules/assembly/scripts/generate_pilon_sort.py
aviary/modules/assembly/scripts/get_binned_reads.py
aviary/modules/assembly/scripts/pool_reads.py
aviary/modules/assembly/scripts/racon_polish.py
aviary/modules/assembly/scripts/run_flye.py
aviary/modules/benchmarking/__init__.py
aviary/modules/benchmarking/scripts/__init__.py
aviary/modules/binning/__init__.py
aviary/modules/binning/scripts/__init__.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/write_vamb_bins.py
aviary/modules/cluster/__init__.py
aviary/modules/cluster/scripts/__init__.py
aviary/modules/quality_control/__init__.py
aviary/modules/quality_control/scripts/__init__.py
aviary/modules/quality_control/scripts/fraction_recovered.py
aviary/modules/quality_control/scripts/run_fastqc.py
aviary/modules/strain_analysis/__init__.py
aviary/modules/strain_analysis/scripts/__init__.py
aviary/modules/strain_analysis/scripts/run_lorikeet.py
aviary/modules/viral_analysis/__init__.py
aviary/modules/viral_analysis/scripts/__init__.py
aviary/scripts/__init__.py
aviary/scripts/create_aviary_webpage.py
aviary/scripts/process_batch.py
aviary/scripts/process_viral_batch.py
aviary/scripts/run_busco.py
aviary/scripts/singlem_reads.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