README.md
setup.py
flye/__build__.py
flye/__init__.py
flye/__version__.py
flye/main.py
flye/six.py
flye.egg-info/PKG-INFO
flye.egg-info/SOURCES.txt
flye.egg-info/dependency_links.txt
flye.egg-info/entry_points.txt
flye.egg-info/top_level.txt
flye/assembly/__init__.py
flye/assembly/assemble.py
flye/assembly/repeat_graph.py
flye/assembly/scaffolder.py
flye/config/__init__.py
flye/config/configurator.py
flye/config/py_cfg.py
flye/config/bin_cfg/asm_corrected_reads.cfg
flye/config/bin_cfg/asm_defaults.cfg
flye/config/bin_cfg/asm_hifi.cfg
flye/config/bin_cfg/asm_raw_reads.cfg
flye/config/bin_cfg/asm_subasm.cfg
flye/config/bin_cfg/nano_r7_homopolymers.mat
flye/config/bin_cfg/nano_r7_substitutions.mat
flye/config/bin_cfg/nano_r94_homopolymers.mat
flye/config/bin_cfg/nano_r94_substitutions.mat
flye/config/bin_cfg/pacbio_homopolymers.mat
flye/config/bin_cfg/pacbio_substitutions.mat
flye/polishing/__init__.py
flye/polishing/alignment.py
flye/polishing/bubbles.py
flye/polishing/consensus.py
flye/polishing/polish.py
flye/repeat_graph/__init__.py
flye/repeat_graph/graph_alignment.py
flye/repeat_graph/repeat_graph.py
flye/short_plasmids/__init__.py
flye/short_plasmids/circular_sequences.py
flye/short_plasmids/plasmids.py
flye/short_plasmids/unmapped_reads.py
flye/short_plasmids/utils.py
flye/tests/__init__.py
flye/tests/test_toy.py
flye/tests/data/ecoli_500kb.fasta
flye/tests/data/ecoli_500kb_reads.fastq.gz
flye/trestle/__init__.py
flye/trestle/divergence.py
flye/trestle/graph_resolver.py
flye/trestle/trestle.py
flye/trestle/trestle_config.py
flye/utils/__init__.py
flye/utils/bytes2human.py
flye/utils/fasta_parser.py
flye/utils/sam_parser.py
flye/utils/utils.py