LICENSE
MANIFEST.in
README.md
setup.py
aviary/__init__.py
aviary/aviary.py
aviary/config/__init__.py
aviary/config/config.py
aviary/envs/__init__.py
aviary/envs/checkm.yaml
aviary/envs/checkm2.yaml
aviary/envs/coverm.yaml
aviary/envs/groopm.yaml
aviary/envs/gtdbtk.yaml
aviary/envs/minimap2.yaml
aviary/envs/singlem.yaml
aviary/envs/webpage.yaml
aviary/modules/Snakefile
aviary/modules/__init__.py
aviary/modules/processor.py
aviary/modules/template_config.yaml
aviary/modules/annotation/__init__.py
aviary/modules/annotation/annotation.smk
aviary/modules/annotation/envs/__init__.py
aviary/modules/annotation/envs/busco.yaml
aviary/modules/annotation/envs/eggnog.yaml
aviary/modules/annotation/scripts/__init__.py
aviary/modules/assembly/__init__.py
aviary/modules/assembly/assembly.smk
aviary/modules/assembly/isolate.smk
aviary/modules/assembly/envs/__init__.py
aviary/modules/assembly/envs/circlator.yaml
aviary/modules/assembly/envs/final_assembly.yaml
aviary/modules/assembly/envs/flye.yaml
aviary/modules/assembly/envs/medaka.yaml
aviary/modules/assembly/envs/megahit.yml
aviary/modules/assembly/envs/mfqe.yaml
aviary/modules/assembly/envs/pilon.yaml
aviary/modules/assembly/envs/polishing.yaml
aviary/modules/assembly/envs/pysam.yaml
aviary/modules/assembly/envs/seqtk.yaml
aviary/modules/assembly/envs/spades.yaml
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/spades_assembly.py
aviary/modules/benchmarking/__init__.py
aviary/modules/benchmarking/benchmarking.smk
aviary/modules/benchmarking/envs/__init__.py
aviary/modules/benchmarking/envs/magpurify.yaml
aviary/modules/benchmarking/scripts/__init__.py
aviary/modules/binning/__init__.py
aviary/modules/binning/binning.smk
aviary/modules/binning/envs/__init__.py
aviary/modules/binning/envs/concoct.yaml
aviary/modules/binning/envs/das_tool.yaml
aviary/modules/binning/envs/maxbin2.yaml
aviary/modules/binning/envs/metabat2.yaml
aviary/modules/binning/envs/rosella.yaml
aviary/modules/binning/envs/semibin.yaml
aviary/modules/binning/envs/vamb.yaml
aviary/modules/binning/scripts/__init__.py
aviary/modules/binning/scripts/das_tool.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/envs/__init__.py
aviary/modules/cluster/envs/pggb.yaml
aviary/modules/cluster/scripts/__init__.py
aviary/modules/quality_control/__init__.py
aviary/modules/quality_control/qc.smk
aviary/modules/quality_control/envs/__init__.py
aviary/modules/quality_control/envs/chopper.yaml
aviary/modules/quality_control/envs/fastqc.yaml
aviary/modules/quality_control/envs/nanoplot.yaml
aviary/modules/quality_control/envs/quast.yaml
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_fastqc.py
aviary/modules/strain_analysis/__init__.py
aviary/modules/strain_analysis/strain_analysis.smk
aviary/modules/strain_analysis/envs/__init__.py
aviary/modules/strain_analysis/envs/lorikeet.yaml
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/viral_analysis.smk
aviary/modules/viral_analysis/envs/__init__.py
aviary/modules/viral_analysis/envs/virfinder.yaml
aviary/modules/viral_analysis/envs/virsorter.yaml
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/run_virfinder.R
aviary/scripts/singlem_appraise.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
test/test_assemble.py
test/test_integration.py
test/test_recover.py
test/test_run_checkm.py