├── .gitattributes ├── .github ├── issue_template.md └── workflows │ └── retest.yaml ├── .gitignore ├── COPYING.txt ├── INSTALL.md ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── rcf ├── recentrifuge ├── __init__.py ├── centrifuge.py ├── centrifuge_io.py ├── clark.py ├── config.py ├── core.py ├── fastq_io.py ├── generic.py ├── img │ ├── favicon.ico │ ├── favicon.uri │ ├── hidden.uri │ ├── loading.uri │ ├── logo-rcf-mini.uri │ ├── recentrifuge.svg │ └── recentrifuge_scaled.svg ├── kraken.py ├── krona.js ├── krona.py ├── lmat.py ├── lmat_io.py ├── mock.py ├── ontology.py ├── params.py ├── rank.py ├── shared_counter.py ├── stats.py ├── taxclass.py ├── taxonomy.py ├── test │ ├── TEST.rcf.html │ ├── TEST.rcf.txt │ ├── TEST.rcf.xlsx │ ├── ctrl1.mck │ ├── ctrl2.mck │ ├── ctrl3.mck │ ├── mock.xlsx │ ├── smpl1.mck │ ├── smpl2.mck │ └── smpl3.mck └── trees.py ├── refafilt ├── refasplit ├── remock ├── requirements.txt ├── retaxdump ├── retest ├── rextraccnt ├── rextract └── setup.py 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