├── .github ├── ISSUE_TEMPLATE │ └── config.yml └── pull_request_template.md ├── HISTORY.md ├── LICENSE.txt ├── README.md ├── demo ├── docs │ ├── demo.md │ └── waafle_webfig1_for_wiki.png ├── input │ ├── demo_contigs.fna │ ├── demo_taxonomy.tsv │ └── demo_waafledb │ │ ├── demo_waafledb.nhr │ │ ├── demo_waafledb.nin │ │ └── demo_waafledb.nsq ├── output │ ├── demo_contigs.blastout │ ├── demo_contigs.gff │ ├── demo_contigs.lgt.tsv │ ├── demo_contigs.no_lgt.tsv │ └── demo_contigs.unclassified.tsv └── output_prodigal │ ├── demo_contigs.prodigal.gff │ ├── demo_contigs.prodigal.lgt.tsv │ ├── demo_contigs.prodigal.no_lgt.tsv │ └── demo_contigs.prodigal.unclassified.tsv ├── setup.py ├── test └── run_demo.sh ├── waafle ├── __init__.py ├── utils.py ├── waafle_genecaller.py ├── waafle_junctions.py ├── waafle_orgscorer.py ├── waafle_qc.py └── waafle_search.py └── website ├── webfig1.png ├── webfig2.png ├── webfig3.png └── website.md /.github/ISSUE_TEMPLATE/config.yml: 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