LICENSE
MANIFEST.in
README.md
setup.py
sphae/__init__.py
sphae/__main__.py
sphae/sphae.CITATION
sphae/sphae.LICENSE
sphae/sphae.VERSION
sphae.egg-info/PKG-INFO
sphae.egg-info/SOURCES.txt
sphae.egg-info/dependency_links.txt
sphae.egg-info/entry_points.txt
sphae.egg-info/requires.txt
sphae.egg-info/top_level.txt
sphae/config/config.yaml
sphae/workflow/Snakefile
sphae/workflow/install.smk
sphae/workflow/envs/checkv.yaml
sphae/workflow/envs/flye.yaml
sphae/workflow/envs/graph.yaml
sphae/workflow/envs/medaka.yaml
sphae/workflow/envs/megahit.yaml
sphae/workflow/envs/pharokka.yaml
sphae/workflow/envs/phynteny.yaml
sphae/workflow/envs/samtools.yaml
sphae/workflow/envs/trimnami.yaml
sphae/workflow/envs/viralverify.yaml
sphae/workflow/rules/1.preflight-database.smk
sphae/workflow/rules/1.preflight.smk
sphae/workflow/rules/2.targets.smk
sphae/workflow/rules/3.qc_qa.smk
sphae/workflow/rules/4.assembly.smk
sphae/workflow/rules/5.checkv.smk
sphae/workflow/rules/5.components.smk
sphae/workflow/rules/5.viralverify.smk
sphae/workflow/rules/6.phage_genome.smk
sphae/workflow/rules/6.stat_join.smk
sphae/workflow/rules/7.pharokka.smk
sphae/workflow/rules/7.phynteny.smk
sphae/workflow/rules/8.final-reporting.smk
sphae/workflow/scripts/components.py
sphae/workflow/scripts/fastg2gfa
sphae/workflow/scripts/joining_stats.py
sphae/workflow/scripts/pick_phage_contigs.py
sphae/workflow/scripts/rename_genomes.py
sphae/workflow/scripts/summary.py
sphae/workflow/scripts/graph_utils/build_utils.py
sphae/workflow/scripts/roblib/__init__.py
sphae/workflow/scripts/roblib/alignments.py
sphae/workflow/scripts/roblib/bcolors.py
sphae/workflow/scripts/roblib/blast.py
sphae/workflow/scripts/roblib/colours.py
sphae/workflow/scripts/roblib/date_parsing.py
sphae/workflow/scripts/roblib/dna.py
sphae/workflow/scripts/roblib/dnadist.py
sphae/workflow/scripts/roblib/file_chooser.py
sphae/workflow/scripts/roblib/functions.py
sphae/workflow/scripts/roblib/genbank.py
sphae/workflow/scripts/roblib/geography.py
sphae/workflow/scripts/roblib/newick.py
sphae/workflow/scripts/roblib/rob_error.py
sphae/workflow/scripts/roblib/seqio_filter.py
sphae/workflow/scripts/roblib/sequences.py
sphae/workflow/scripts/roblib/stats.py
sphae/workflow/scripts/roblib/strings.py
sphae/workflow/scripts/roblib/translate.py
tests/test_sphae.py