├── Dockerfile ├── LICENSE ├── README.md ├── bin ├── DeepRepeat.py ├── data │ ├── config │ │ ├── fast5_path.config │ │ ├── fast5_path_1.config │ │ └── fast5_path_multi.config │ ├── plasmid_trf.bed │ ├── trf.v0.bed │ └── wg_trf.cag.bed └── scripts │ ├── BamReader.c │ ├── BamReader.h │ ├── ComFunction.c │ ├── ComFunction.h │ ├── ComOption.c │ ├── ComOption.h │ ├── ComStruct.h │ ├── DeepNanoRepeat.c │ ├── Fast5Index.c │ ├── Fast5Index.h │ ├── Fast5Reader.c │ ├── Fast5Reader.h │ ├── IndexF5files │ ├── IndexF5files.c │ ├── RepeatFeatExtract.c │ ├── RepeatFeatExtract.h │ ├── Repeat_CNN_Prediction_model.py │ ├── Repeat_CNN_Prediction_motif_gen2.py │ ├── Repeat_CNN_Train_genome_motif2.py │ ├── Repeat_CNN_model_motif2.py │ ├── genomic1FE │ ├── genomic1FE.c │ ├── myGaussianMixtureModel.py │ └── myHeader.py ├── docs ├── DeepRepeat_flowchart.png ├── Reproducibility.md ├── TGC_repeat.png └── mismatch_rate.png ├── environment.yml └── tools ├── get_bam.py └── get_fq_barcode.py /Dockerfile: 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