.gitignore
CITATION.cff
Changes.md
Dockerfile
LICENSE
MANIFEST.in
README.md
environment.yml
pyproject.toml
requirements.txt
sphae.sh
.github/workflows/python-publish.yml
.github/workflows/testing.yml
.vscode/settings.json
logo/sphae.png
logo/sphae_steps.png
logo/sphaedark.png
misc/README.md
misc/merging_output.py
misc/num_cds.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/Snakefile-annot
sphae/workflow/install.smk
sphae/workflow/envs/checkv.yaml
sphae/workflow/envs/filtlong.yaml
sphae/workflow/envs/flye.yaml
sphae/workflow/envs/graph.yaml
sphae/workflow/envs/medaka.yaml
sphae/workflow/envs/megahit.yaml
sphae/workflow/envs/phageterm.yaml
sphae/workflow/envs/pharokka.yaml
sphae/workflow/envs/phold.yaml
sphae/workflow/envs/phynteny.yaml
sphae/workflow/envs/qc.yaml
sphae/workflow/envs/rasusa.yaml
sphae/workflow/envs/samtools.yaml
sphae/workflow/envs/trees.yaml
sphae/workflow/envs/viralverify.yaml
sphae/workflow/rules/1.preflight-annot.smk
sphae/workflow/rules/1.preflight.smk
sphae/workflow/rules/10.trees.smk
sphae/workflow/rules/11.final-reporting.smk
sphae/workflow/rules/2.targets-annot.smk
sphae/workflow/rules/2.targets.smk
sphae/workflow/rules/3.qc_qa.smk
sphae/workflow/rules/4.assembly.smk
sphae/workflow/rules/4.assembly_no_medaka.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.phageterm.smk
sphae/workflow/rules/7.pharokka.smk
sphae/workflow/rules/789.annot.smk
sphae/workflow/rules/8.phold.smk
sphae/workflow/rules/9.phynteny.smk
sphae/workflow/scripts/components.py
sphae/workflow/scripts/fastg2gfa
sphae/workflow/scripts/get_marker_ids.py
sphae/workflow/scripts/joining_stats.py
sphae/workflow/scripts/pick_phage_contigs.py
sphae/workflow/scripts/split_fasta.py
sphae/workflow/scripts/summary-annot.py
sphae/workflow/scripts/summary.py
sphae/workflow/scripts/summary_annot_functions.py
sphae/workflow/scripts/summary_functions.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
tests/data/README.md
tests/data/genome/test_genome.fasta
tests/data/illumina-subset/SRR16219309_R1.fastq.gz
tests/data/illumina-subset/SRR16219309_R2.fastq.gz
tests/data/illumina-subset/test_R1.fastq.gz
tests/data/illumina-subset/test_R2.fastq.gz
tests/data/nanopore-subset/nanoreads.fastq
tests/db/pharokka_db
tests/db/phold
tests/db/phynteny_models_zenodo
tests/db/Pfam35.0/Pfam-A.hmm.gz
tests/db/checkv-db-v1.5/genome_db/checkv_reps.dmnd
tests/db/checkv-db-v1.5/genome_db/checkv_reps.tsv