├── LICENSE ├── README.md ├── default_configfile.yml ├── environment.yml ├── eukdetect ├── __init__.py ├── __pycache__ │ └── __init__.cpython-36.pyc ├── bam_to_pid.py ├── combine_rpks_eukfrac.py ├── count_primary_and_secondary.py ├── count_primary_and_secondary_eukfrac.py ├── count_primary_and_secondary_sehits.py ├── eukdb_config_create.py └── runall.py ├── eukdetect_pipeline_schematic.pdf ├── rules ├── eukdetect.rules ├── eukdetect_eukfrac.rules └── eukdetect_sehits.rules ├── setup.py └── tests ├── configfile_for_tests.yml ├── test_R1.fastq.gz ├── test_R2.fastq.gz └── test_eukdetect.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allind/EukDetect/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/allind/EukDetect/HEAD/README.md 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