├── .gitignore ├── .ycm_extra_conf.py ├── LICENSE ├── Makefile ├── README.md ├── bin ├── .gitkeep └── flye ├── docs ├── FAQ.md ├── INSTALL.md ├── NEWS.md ├── USAGE.md └── graph_example.png ├── flye ├── .main.py.swo ├── __build__.py ├── __init__.py ├── __version__.py ├── assembly │ ├── __init__.py │ ├── assemble.py │ ├── repeat_graph.py │ └── scaffolder.py ├── config │ ├── __init__.py │ ├── bin_cfg │ │ ├── asm_corrected_reads.cfg │ │ ├── asm_defaults.cfg │ │ ├── asm_hifi.cfg │ │ ├── asm_nano_hq.cfg │ │ ├── asm_raw_reads.cfg │ │ ├── asm_subasm.cfg │ │ ├── nano_r94_g36_homopolymers.mat │ │ ├── nano_r94_g36_substitutions.mat │ │ ├── nano_r94_homopolymers.mat │ │ ├── nano_r94_substitutions.mat │ │ ├── pacbio_chm13_homopolymers.mat │ │ ├── pacbio_chm13_substitutions.mat │ │ ├── pacbio_homopolymers.mat │ │ └── pacbio_substitutions.mat │ ├── configurator.py │ └── py_cfg.py ├── main.py ├── polishing │ ├── __init__.py │ ├── alignment.py │ ├── bubbles.py │ ├── consensus.py │ └── polish.py ├── repeat_graph │ ├── __init__.py │ ├── graph_alignment.py │ └── repeat_graph.py ├── short_plasmids │ ├── __init__.py │ ├── circular_sequences.py │ ├── plasmids.py │ ├── unmapped_reads.py │ └── utils.py ├── six.py ├── tests │ ├── __init__.py │ ├── data │ │ ├── ecoli_500kb.fasta │ │ ├── ecoli_500kb_reads.fastq.gz │ │ └── ecoli_500kb_reads_hifi.fastq.gz │ └── test_toy.py ├── trestle │ ├── __init__.py │ ├── divergence.py │ ├── graph_resolver.py │ ├── trestle.py │ └── trestle_config.py └── utils │ ├── __init__.py │ ├── bytes2human.py │ ├── fasta_parser.py │ ├── sam_parser.py │ └── utils.py ├── lib ├── interval_tree │ ├── IntervalTree.h │ ├── LICENSE │ └── README.md ├── lemon │ ├── AUTHORS │ ├── INSTALL │ ├── LICENSE │ ├── NEWS │ ├── README │ └── lemon │ │ ├── adaptors.h │ │ ├── arg_parser.h │ │ ├── assert.h │ │ ├── bellman_ford.h │ │ ├── bfs.h │ │ ├── bin_heap.h │ │ ├── binomial_heap.h │ │ ├── bits │ │ ├── alteration_notifier.h │ │ ├── array_map.h │ │ ├── bezier.h │ │ ├── default_map.h │ │ ├── edge_set_extender.h │ │ ├── enable_if.h │ │ ├── graph_adaptor_extender.h │ │ ├── graph_extender.h │ │ ├── lock.h │ │ ├── map_extender.h │ │ ├── path_dump.h │ │ ├── solver_bits.h │ │ ├── traits.h │ │ ├── variant.h │ │ ├── vector_map.h │ │ └── windows.h │ │ ├── bucket_heap.h │ │ ├── capacity_scaling.h │ │ ├── cbc.h │ │ ├── christofides_tsp.h │ │ ├── circulation.h │ │ ├── clp.h │ │ ├── color.h │ │ ├── concept_check.h │ │ ├── concepts │ │ ├── bpgraph.h │ │ ├── digraph.h │ │ ├── graph.h │ │ ├── graph_components.h │ │ ├── heap.h │ │ ├── maps.h │ │ └── path.h │ │ ├── config.h │ │ ├── connectivity.h │ │ ├── core.h │ │ ├── cost_scaling.h │ │ ├── counter.h │ │ ├── cplex.h │ │ ├── cycle_canceling.h │ │ ├── dfs.h │ │ ├── dheap.h │ │ ├── dijkstra.h │ │ ├── dim2.h │ │ ├── dimacs.h │ │ ├── edge_set.h │ │ ├── edmonds_karp.h │ │ ├── elevator.h │ │ ├── error.h │ │ ├── euler.h │ │ ├── fib_heap.h │ │ ├── fractional_matching.h │ │ ├── full_graph.h │ │ ├── glpk.h │ │ ├── gomory_hu.h │ │ ├── graph_to_eps.h │ │ ├── greedy_tsp.h │ │ ├── grid_graph.h │ │ ├── grosso_locatelli_pullan_mc.h │ │ ├── hao_orlin.h │ │ ├── hartmann_orlin_mmc.h │ │ ├── howard_mmc.h │ │ ├── hypercube_graph.h │ │ ├── insertion_tsp.h │ │ ├── karp_mmc.h │ │ ├── kruskal.h │ │ ├── lgf_reader.h │ │ ├── lgf_writer.h │ │ ├── list_graph.h │ │ ├── lp.h │ │ ├── lp_base.h │ │ ├── lp_skeleton.h │ │ ├── maps.h │ │ ├── matching.h │ │ ├── math.h │ │ ├── max_cardinality_search.h │ │ ├── min_cost_arborescence.h │ │ ├── nagamochi_ibaraki.h │ │ ├── nauty_reader.h │ │ ├── nearest_neighbor_tsp.h │ │ ├── network_simplex.h │ │ ├── opt2_tsp.h │ │ ├── pairing_heap.h │ │ ├── path.h │ │ ├── planarity.h │ │ ├── preflow.h │ │ ├── quad_heap.h │ │ ├── radix_heap.h │ │ ├── radix_sort.h │ │ ├── random.h │ │ ├── smart_graph.h │ │ ├── soplex.h │ │ ├── static_graph.h │ │ ├── suurballe.h │ │ ├── time_measure.h │ │ ├── tolerance.h │ │ └── unionfind.h ├── libcuckoo │ ├── LICENSE │ ├── README.md │ ├── cuckoohash_config.hh │ ├── cuckoohash_map.hh │ ├── cuckoohash_util.hh │ └── libcuckoo_bucket_container.hh ├── minimap2 │ ├── FAQ.md │ ├── LICENSE.txt │ ├── MANIFEST.in │ ├── Makefile │ ├── Makefile.simde │ ├── NEWS.md │ ├── README.md │ ├── align.c │ ├── bseq.c │ ├── bseq.h │ ├── chain.c │ ├── cookbook.md │ ├── esterr.c │ ├── example.c │ ├── format.c │ ├── hit.c │ ├── index.c │ ├── kalloc.c │ ├── kalloc.h │ ├── kdq.h │ ├── ketopt.h │ ├── khash.h │ ├── krmq.h │ ├── kseq.h │ ├── ksort.h │ ├── ksw2.h │ ├── ksw2_dispatch.c │ ├── ksw2_extd2_sse.c │ ├── ksw2_exts2_sse.c │ ├── ksw2_extz2_sse.c │ ├── ksw2_ll_sse.c │ ├── kthread.c │ ├── kthread.h │ ├── kvec.h │ ├── lchain.c │ ├── main.c │ ├── map.c │ ├── minimap.h │ ├── minimap2.1 │ ├── misc.c │ ├── misc │ │ ├── README.md │ │ ├── mmphase.js │ │ └── paftools.js │ ├── mmpriv.h │ ├── options.c │ ├── pe.c │ ├── python │ │ ├── README.rst │ │ ├── cmappy.h │ │ ├── cmappy.pxd │ │ ├── mappy.pyx │ │ └── minimap2.py │ ├── sdust.c │ ├── sdust.h │ ├── seed.c │ ├── setup.py │ ├── sketch.c │ ├── splitidx.c │ ├── sse2neon │ │ └── emmintrin.h │ └── test │ │ ├── MT-human.fa │ │ ├── MT-orang.fa │ │ ├── q-inv.fa │ │ ├── q2.fa │ │ ├── t-inv.fa │ │ └── t2.fa └── samtools-1.9 │ ├── AUTHORS │ ├── ChangeLog.old │ ├── INSTALL │ ├── LICENSE │ ├── Makefile │ ├── Makefile.mingw │ ├── NEWS │ ├── README │ ├── bam.c │ ├── bam.h │ ├── bam2bcf.c │ ├── bam2bcf.h │ ├── bam2bcf_indel.c │ ├── bam2depth.c │ ├── bam_addrprg.c │ ├── bam_aux.c │ ├── bam_cat.c │ ├── bam_color.c │ ├── bam_endian.h │ ├── bam_flags.c │ ├── bam_import.c │ ├── bam_index.c │ ├── bam_lpileup.c │ ├── bam_lpileup.h │ ├── bam_markdup.c │ ├── bam_mate.c │ ├── bam_md.c │ ├── bam_plbuf.c │ ├── bam_plbuf.h │ ├── bam_plcmd.c │ ├── bam_quickcheck.c │ ├── bam_reheader.c │ ├── bam_rmdup.c │ ├── bam_rmdupse.c │ ├── bam_sort.c │ ├── bam_split.c │ ├── bam_stat.c │ ├── bam_tview.c │ ├── bam_tview.h │ ├── bam_tview_curses.c │ ├── bam_tview_html.c │ ├── bamshuf.c │ ├── bamtk.c │ ├── bedcov.c │ ├── bedidx.c │ ├── bedidx.h │ ├── config.h.in │ ├── config.mk.in │ ├── configure │ ├── configure.ac │ ├── cut_target.c │ ├── dict.c │ ├── faidx.c │ ├── htslib-1.9 │ ├── INSTALL │ ├── LICENSE │ ├── Makefile │ ├── NEWS │ ├── README │ ├── bcf_sr_sort.c │ ├── bcf_sr_sort.h │ ├── bgzf.c │ ├── bgzip.1 │ ├── bgzip.c │ ├── config.h.in │ ├── config.mk.in │ ├── configure │ ├── configure.ac │ ├── cram │ │ ├── cram.h │ │ ├── cram_codecs.c │ │ ├── cram_codecs.h │ │ ├── cram_decode.c │ │ ├── cram_decode.h │ │ ├── cram_encode.c │ │ ├── cram_encode.h │ │ ├── cram_external.c │ │ ├── cram_index.c │ │ ├── cram_index.h │ │ ├── cram_io.c │ │ ├── cram_io.h │ │ ├── cram_samtools.c │ │ ├── cram_samtools.h │ │ ├── cram_stats.c │ │ ├── cram_stats.h │ │ ├── cram_structs.h │ │ ├── files.c │ │ ├── mFILE.c │ │ ├── mFILE.h │ │ ├── misc.h │ │ ├── open_trace_file.c │ │ ├── open_trace_file.h │ │ ├── os.h │ │ ├── pooled_alloc.c │ │ ├── pooled_alloc.h │ │ ├── rANS_byte.h │ │ ├── rANS_static.c │ │ ├── rANS_static.h │ │ ├── sam_header.c │ │ ├── sam_header.h │ │ ├── string_alloc.c │ │ └── string_alloc.h │ ├── errmod.c │ ├── faidx.5 │ ├── faidx.c │ ├── hfile.c │ ├── hfile_gcs.c │ ├── hfile_internal.h │ ├── hfile_libcurl.c │ ├── hfile_net.c │ ├── hfile_s3.c │ ├── hts.c │ ├── hts_internal.h │ ├── hts_os.c │ ├── htsfile.1 │ ├── htsfile.c │ ├── htslib.mk │ ├── htslib.pc.in │ ├── htslib │ │ ├── bgzf.h │ │ ├── cram.h │ │ ├── faidx.h │ │ ├── hfile.h │ │ ├── hts.h │ │ ├── hts_defs.h │ │ ├── hts_endian.h │ │ ├── hts_log.h │ │ ├── hts_os.h │ │ ├── kbitset.h │ │ ├── kfunc.h │ │ ├── khash.h │ │ ├── khash_str2int.h │ │ ├── klist.h │ │ ├── knetfile.h │ │ ├── kseq.h │ │ ├── ksort.h │ │ ├── kstring.h │ │ ├── regidx.h │ │ ├── sam.h │ │ ├── synced_bcf_reader.h │ │ ├── tbx.h │ │ ├── thread_pool.h │ │ ├── vcf.h │ │ ├── vcf_sweep.h │ │ └── vcfutils.h │ ├── htslib_vars.mk │ ├── kfunc.c │ ├── knetfile.c │ ├── kstring.c │ ├── m4 │ │ └── hts_prog_cc_warnings.m4 │ ├── md5.c │ ├── multipart.c │ ├── os │ │ ├── lzma_stub.h │ │ └── rand.c │ ├── plugin.c │ ├── probaln.c │ ├── realn.c │ ├── regidx.c │ ├── sam.5 │ ├── sam.c │ ├── synced_bcf_reader.c │ ├── tabix.1 │ ├── tabix.c │ ├── tbx.c │ ├── textutils.c │ ├── textutils_internal.h │ ├── thread_pool.c │ ├── thread_pool_internal.h │ ├── vcf.5 │ ├── vcf.c │ ├── vcf_sweep.c │ ├── vcfutils.c │ └── version.sh │ ├── install-sh │ ├── lz4 │ ├── LICENSE │ ├── lz4.c │ └── lz4.h │ ├── m4 │ ├── ax_with_curses.m4 │ └── ax_with_htslib.m4 │ ├── misc │ ├── HmmGlocal.java │ ├── ace2sam.c │ ├── blast2sam.pl │ ├── bowtie2sam.pl │ ├── export2sam.pl │ ├── interpolate_sam.pl │ ├── maq2sam.c │ ├── md5fa.c │ ├── md5sum-lite.c │ ├── novo2sam.pl │ ├── plot-bamstats │ ├── psl2sam.pl │ ├── r2plot.lua │ ├── sam2vcf.pl │ ├── samtools.pl │ ├── samtools_tab_completion │ ├── seq_cache_populate.pl │ ├── soap2sam.pl │ ├── varfilter.py │ ├── vcfutils.lua │ ├── wgsim.1 │ ├── wgsim.c │ ├── wgsim_eval.pl │ └── zoom2sam.pl │ ├── padding.c │ ├── phase.c │ ├── sam.c │ ├── sam.h │ ├── sam_header.c │ ├── sam_header.h │ ├── sam_opts.c │ ├── sam_opts.h │ ├── sam_utils.c │ ├── sam_view.c │ ├── sample.c │ ├── sample.h │ ├── samtools.1 │ ├── samtools.h │ ├── stats.c │ ├── stats_isize.c │ ├── stats_isize.h │ ├── tmp_file.c │ ├── tmp_file.h │ ├── version.sh │ └── win32 │ ├── xcurses.h │ ├── zconf.h │ └── zlib.h ├── requirements.txt ├── setup.py └── src ├── Makefile ├── assemble ├── chimera.cpp ├── chimera.h ├── extender.cpp ├── extender.h ├── main_assemble.cpp ├── parameters_estimator.cpp └── parameters_estimator.h ├── common ├── bfcontainer.h ├── config.h ├── disjoint_set.h ├── logger.h ├── matrix.h ├── memory_info.h ├── parallel.h ├── progress_bar.h └── utils.h ├── contigger ├── contig_extender.cpp ├── contig_extender.h └── main_contigger.cpp ├── main.cpp ├── polishing ├── alignment.cpp ├── alignment.h ├── bubble.h ├── bubble_processor.cpp ├── bubble_processor.h ├── dinucleotide_fixer.cpp ├── dinucleotide_fixer.h ├── general_polisher.cpp ├── general_polisher.h ├── homo_polisher.cpp ├── homo_polisher.h ├── 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