├── .gitmodules ├── LICENSE ├── README.md ├── changelinewidth.py ├── evaluation ├── Annotation_Load.py ├── Annotation_formats.py ├── Eval_NanoSim_data.py ├── Eval_PBsim_data.py ├── Eval_real_data.py ├── GetSingleSpliceTranID.py ├── cal_NanoSim_background.py ├── cal_PBsim_background.py ├── data_evaluation.md ├── fastqparser.py ├── part_cal.py └── utility_sam.py ├── img ├── deSALT_fig.png └── deSALT_pipeline.jpg ├── simulation ├── Annotation_grouping.py ├── Example │ ├── pipeline_simulation.sh │ ├── simulate_CCS.sh │ ├── simulate_CLR.sh │ ├── simulate_NS_ONT.sh │ ├── simulate_ONT1D.sh │ ├── simulate_ONT2D.sh │ ├── simulate_PS_ONT.sh │ └── tran_qname.py ├── Sim_data_generation.md ├── generate_transcriptome.py └── pbsim-1.0.3-Linux-amd64 │ ├── .deps │ └── pbsim.Po │ ├── AUTHORS │ ├── COPYING │ ├── ChangeLog │ ├── Linux-amd64 │ ├── .deps │ │ └── pbsim.Po │ └── bin │ │ └── pbsim │ ├── NEWS │ ├── README │ ├── data │ ├── model_qc_ccs │ └── model_qc_clr │ └── sample │ ├── sample.fasta │ └── sample.fastq └── src ├── Annotation_Load.py ├── Makefile ├── aln_2pass.c ├── aln_2pass.h ├── binarys_qsort.c ├── binarys_qsort.h ├── bit_operation.c ├── bit_operation.h ├── bseq.c ├── bseq.h ├── deBGA ├── deBGA-master ├── LandauVishkin.c ├── LandauVishkin.h ├── Makefile ├── binarys_qsort.h ├── bit_operation.c ├── bit_operation.h ├── index_build.c ├── index_build.h ├── kseq.h ├── ksw.c ├── ksw.h ├── load_input.c ├── load_input.h ├── main.c ├── seed_ali_core.c └── seed_ali_p.h ├── desalt_index.c ├── desalt_index.h ├── format.c ├── format.h ├── graph.c ├── graph.h ├── hash_index.c ├── hash_index.h ├── kalloc.c ├── kalloc.h ├── kseq.h ├── ksw2.h ├── ksw2_dispatch.c ├── ksw2_extd2_sse.c ├── ksw2_exts2_sse.c ├── ksw2_extz2_sse.c ├── ksw2_ll_sse.c ├── ktime.c ├── ktime.h ├── load_unipath_size.c ├── load_unipath_size.h ├── main.c ├── read_seeding.c ├── read_seeding.h ├── splic_junction.c └── splic_junction.h /.gitmodules: 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