├── CMakeLists.txt ├── README.md ├── SOAP_post_process.py ├── deps ├── cxxopts │ ├── .gitignore │ ├── .idea │ │ ├── codeStyles │ │ │ ├── Project.xml │ │ │ └── codeStyleConfig.xml │ │ ├── cxxopts.iml │ │ ├── dictionaries │ │ │ └── yanesl.xml │ │ ├── misc.xml │ │ ├── modules.xml │ │ ├── vcs.xml │ │ └── workspace.xml │ ├── .travis.yml │ ├── CHANGELOG.md │ ├── CMakeLists.txt │ ├── INSTALL │ ├── LICENSE │ ├── README.md │ ├── cmake-build-debug │ │ ├── cxxopts-config-version.cmake │ │ ├── cxxopts-config.cmake │ │ ├── cxxopts-targets.cmake │ │ ├── cxxopts.cbp │ │ ├── src │ │ │ └── example │ │ └── test │ │ │ └── options_test │ ├── cxxopts-config.cmake.in │ ├── include │ │ └── cxxopts.hpp │ ├── src │ │ ├── .gitignore │ │ ├── CMakeLists.txt │ │ └── example.cpp │ └── test │ │ ├── .gitignore │ │ ├── CMakeLists.txt │ │ ├── add-subdirectory-test │ │ └── CMakeLists.txt │ │ ├── catch.hpp │ │ ├── find-package-test │ │ └── CMakeLists.txt │ │ ├── link_a.cpp │ │ ├── link_b.cpp │ │ ├── main.cpp │ │ └── options.cpp ├── flash │ ├── .idea │ │ ├── codeStyles │ │ │ ├── Project.xml │ │ │ └── codeStyleConfig.xml │ │ ├── dictionaries │ │ │ └── yanesl.xml │ │ ├── flash.iml │ │ ├── misc.xml │ │ ├── modules.xml │ │ ├── vcs.xml │ │ └── workspace.xml │ ├── CMakeLists.txt │ ├── COPYING │ ├── Makefile │ ├── NEWS │ ├── README │ ├── cmake-build-debug │ │ ├── CMakeCache.txt │ │ ├── CMakeFiles │ │ │ ├── 3.13.4 │ │ │ │ ├── CMakeCCompiler.cmake │ │ │ │ ├── CMakeDetermineCompilerABI_C.bin │ │ │ │ ├── CMakeSystem.cmake │ │ │ │ └── CompilerIdC │ │ │ │ │ ├── CMakeCCompilerId.c │ │ │ │ │ └── a.out │ │ │ ├── CMakeDirectoryInformation.cmake │ │ │ ├── CMakeOutput.log │ │ │ ├── Makefile.cmake │ │ │ ├── Makefile2 │ │ │ ├── TargetDirectories.txt │ │ │ ├── clion-environment.txt │ │ │ ├── clion-log.txt │ │ │ ├── cmake.check_cache │ │ │ ├── feature_tests.bin │ │ │ ├── feature_tests.c │ │ │ ├── flash.dir │ │ │ │ ├── C.includecache │ │ │ │ ├── DependInfo.cmake │ │ │ │ ├── build.make │ │ │ │ ├── cmake_clean.cmake │ │ │ │ ├── combine_reads.c.o │ │ │ │ ├── depend.internal │ │ │ │ ├── depend.make │ │ │ │ ├── flags.make │ │ │ │ ├── flash.c.o │ │ │ │ ├── iostream.c.o │ │ │ │ ├── link.txt │ │ │ │ ├── progress.make │ │ │ │ ├── read_io.c.o │ │ │ │ ├── read_queue.c.o │ │ │ │ ├── read_util.c.o │ │ │ │ └── util.c.o │ │ │ └── progress.marks │ │ ├── Makefile │ │ ├── cmake_install.cmake │ │ ├── flash │ │ └── flash.cbp │ ├── combine_reads.c │ ├── combine_reads.h │ ├── flash.c │ ├── iostream.c │ ├── iostream.h │ ├── read.h │ ├── read_io.c │ ├── read_io.h │ ├── read_queue.c │ ├── read_queue.h │ ├── read_util.c │ ├── util.c │ └── util.h ├── nextclip │ ├── .gitignore │ ├── CMakeLists.txt │ ├── LICENSE │ ├── Makefile │ ├── README.md │ ├── examples │ │ ├── ReadMe.md │ │ ├── configure │ │ │ └── LIB1468.txt │ │ ├── reads │ │ │ ├── LIB1468part_ATCACG_L001_R1_001.fastq │ │ │ └── LIB1468part_ATCACG_L001_R2_001.fastq │ │ ├── references │ │ │ └── AL645882.fasta │ │ └── reports │ │ │ ├── LIB1468.pdf │ │ │ └── LIB4659.pdf │ ├── include │ │ ├── binary_kmer.h │ │ ├── element.h │ │ ├── flags.h │ │ ├── global.h │ │ ├── hash_table.h │ │ ├── hash_value.h │ │ ├── logger.h │ │ ├── nucleotide.h │ │ └── seq.h │ ├── nextclipmanual.pdf │ ├── scripts │ │ ├── index_bwa.sh │ │ ├── nextclip_index_reference.pl │ │ ├── nextclip_lmp_analysis.pl │ │ ├── nextclip_make_report.pl │ │ ├── nextclip_plot_duplication.R │ │ ├── nextclip_plot_gc.R │ │ ├── nextclip_plot_graphs.sh │ │ ├── nextclip_plot_inserts.R │ │ ├── nextclip_plot_lengths.R │ │ ├── nextclip_plot_pair_lengths.R │ │ └── nextclip_sam_parse.pl │ └── src │ │ ├── binary_kmer.c │ │ ├── element.c │ │ ├── hash_table.c │ │ ├── hash_value.c │ │ ├── logger.c │ │ └── nextclip.c └── soap_scaffolder │ ├── CMakeLists.txt │ ├── LICENSE │ ├── Makefile │ ├── arc.c │ ├── attachPEinfo.c │ ├── change.log │ ├── check.c │ ├── connect.c │ ├── darray.c │ ├── dfib.c │ ├── dfibHeap.c │ ├── fib.c │ ├── fibHeap.c │ ├── hashFunction.c │ ├── inc │ ├── bgzf.h │ ├── check.h │ ├── darray.h │ ├── def.h │ ├── def2.h │ ├── dfib.h │ ├── dfibHeap.h │ ├── dfibpriv.h │ ├── extfunc.h │ ├── extfunc2.h │ ├── extvab.h │ ├── faidx.h │ ├── fib.h │ ├── fibHeap.h │ ├── fibpriv.h │ ├── glf.h │ ├── global.h │ ├── kmerhash.h │ ├── knetfile.h │ ├── kstring.h │ ├── newhash.h │ ├── razf.h │ ├── sam_header.h │ ├── stack.h │ ├── stdinc.h │ ├── types.h │ ├── xcurses.h │ ├── zconf.h │ └── zlib.h │ ├── kmer.c │ ├── lib.c │ ├── loadGraph.c │ ├── loadPreGraph.c │ ├── localAsm.c │ ├── make.sh │ ├── makeclean.sh │ ├── map.c │ ├── mem_manager.c │ ├── newhash.c │ ├── orderContig.c │ ├── output_contig.c │ ├── output_scaffold.c │ ├── prepare.c │ ├── prlHashCtg.c │ ├── prlRead2Ctg.c │ ├── prlReadFillGap.c │ ├── readseq1by1.c │ ├── scaffold.c │ ├── searchPath.c │ ├── seperateScaff.pl │ ├── seq.c │ └── stack.c ├── images ├── contigs_fac.png ├── fastqc.png ├── lmp_vs_pe-main.mx.spectra-cn.png ├── lmp_vs_pe.png ├── lmp_vs_pe_k27-main.mx.density.png ├── lmp_vs_pe_spectra_mx.png ├── pe_vs_contigs_k27-main.mx.spectra-cn.png 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