├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── deepbinner-runner.py ├── deepbinner ├── __init__.py ├── balance.py ├── bin.py ├── classify.py ├── deepbinner.py ├── dtw │ ├── dtw.cpp │ └── dtw.h ├── dtw_semi_global.py ├── help_formatter.py ├── load_fast5s.py ├── misc.py ├── network_architecture.py ├── prep.py ├── prep_functions.py ├── prep_native_end.py ├── prep_native_start.py ├── prep_rapid_start.py ├── realtime.py ├── refine.py ├── sequences.py ├── signals.py ├── train_network.py ├── trim_signal.py └── version.py ├── images ├── logo-deepsea.png ├── logo-stripes-dna.png ├── logo-stripes.png └── tensorflow.png ├── models ├── EXP-NBD103_read_ends ├── EXP-NBD103_read_starts ├── README.md └── SQK-RBK004_read_starts ├── requirements.txt ├── sample_reads.tar.gz ├── scripts ├── assign_reads_to_reference.py └── process_scrappie_squiggle.py ├── setup.py └── tests ├── __init__.py ├── fast5_files ├── 5210_N128870_20180511_FAH70336_MN20200_sequencing_run_057_Deepbinner_amplicon_43629_read_11206_ch_157_strand.fast5 ├── 5210_N128870_20180511_FAH70336_MN20200_sequencing_run_057_Deepbinner_amplicon_43629_read_13863_ch_212_strand.fast5 ├── 5210_N128870_20180511_FAH70336_MN20200_sequencing_run_057_Deepbinner_amplicon_43629_read_14150_ch_70_strand.fast5 ├── 5210_N128870_20180511_FAH70336_MN20200_sequencing_run_057_Deepbinner_amplicon_43629_read_14637_ch_372_strand.fast5 ├── 5210_N128870_20180511_FAH70336_MN20200_sequencing_run_057_Deepbinner_amplicon_43629_read_20576_ch_70_strand.fast5 ├── 5210_N128870_20180511_FAH70336_MN20200_sequencing_run_057_Deepbinner_amplicon_43629_read_22801_ch_102_strand.fast5 └── FAK33493_1336eeb8050cb1ca93d41712cf8e817516306473_1000000.fast5 ├── multi_read_fast5_files ├── FAK33493_2dac03b8dc7b3757bdcf3b4fed263b60fa5da102_1000.fast5 ├── FAK33493_2dac03b8dc7b3757bdcf3b4fed263b60fa5da102_1001.fast5 └── FAK33493_2dac03b8dc7b3757bdcf3b4fed263b60fa5da102_1002.fast5 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