├── .gitattributes ├── .gitignore ├── Makefile ├── README.md ├── bash_scripts ├── HPRC_assessAsemblyCompletness.wdl ├── asmgene_hap.sh ├── asmgene_pri.sh ├── chopper.sh ├── chopper_long_repeats.sh ├── countT2T.sh ├── dipcall.sh ├── hifiasm_analysis.sh ├── hifiasm_r555_trial.sh ├── hifiasm_trial.sh ├── hifiasm_trial_ec.sh ├── map_mm_noncontained.sh ├── minigraph.sh ├── minimapAllToAllCigar.sh ├── quast_eval_hap.sh ├── quast_pri.sh ├── real_reads.sh ├── rescued_contained_reads.sh ├── simulate.sh ├── switch_error.sh ├── yak_qv_hap.sh └── yak_qv_pri.sh ├── chop.hpp ├── kseq.h ├── main.cpp ├── overlap.hpp ├── paf.hpp ├── param.hpp ├── read.hpp ├── repeat.hpp ├── run.sh └── split_naive.cpp /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/at-cg/RAFT/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: 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