├── .gitignore ├── INSTALL.md ├── LICENSE ├── README.md ├── demo ├── SRAssembler.conf ├── input │ ├── 0README │ ├── AT1G01950.cdna │ ├── LOC_Os06g04560.pep │ ├── reads1_1000.fq │ ├── reads1_200.fq │ ├── reads2_1000.fq │ ├── reads2_200.fq │ ├── taboo.dna │ └── taboo.pep ├── libraries_200bp.conf ├── libraries_200bp_1kb.conf ├── standards │ ├── testout1.html │ ├── testout10.html │ ├── testout11.html │ ├── testout12.html │ ├── testout13.html │ ├── testout14.html │ ├── testout2.html │ ├── testout3.html │ ├── testout4.html │ ├── testout5.1.html │ ├── testout5.2.html │ ├── testout5.3.html │ ├── testout6.html │ ├── testout7.html │ ├── testout8.html │ ├── testout9.ano │ └── testout9.html ├── xquicktest └── xtest ├── sra.def └── src ├── AbyssAssembler.cpp ├── AbyssAssembler.h ├── Aligner.cpp ├── Aligner.h ├── Assembler.cpp ├── Assembler.h ├── Const.h ├── GSQAligner.cpp ├── GSQAligner.h ├── GTHAligner.cpp ├── GTHAligner.h ├── GeneFinder.cpp ├── GeneFinder.h ├── Library.cpp ├── Library.h ├── 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