[5]-3FILElistof hap1/paternal read names[]-4FILElistof hap2/maternal read names[]--t-occ INT force remove unitigswith>INT unexpected haplotype-specific reads;ignore graph topology;[60]Purge-dups:-l INT purge level.0:no purging;1:light;2/3:aggressive[0fortrio;3forunzip]-s FLOAT ...
Hifiasm can purge duplications between haplotigs without relying on third-party tools such as purge_dups. Hifiasm does not need polishing tools like pilon or racon, either. This simplifies the assembly pipeline and saves running time. Hifiasm is fast. It can assemble a human genome in half a...
[%s] ERROR\n", __func__); exit(1); } } } for (i = 0; i < ug->g->n_arc; ++i) { // the Link lines in GFA uint32_t u = ug->g->arc[i].ul>>32, v = ug->g->arc[i].v; fprintf(fp, "L\t%s%.6d%c\t%c\t%s%.6d%c\t%c\t%dM\tL1:i:%d\n", "utg",...
hifiasm_dev_debug doc-update dev-lh3 hifiasm-v0.14 for_adapter hifiasm_high_het contain flt-p chain-tune 0.18.5 0.18.4 0.18.2 0.18.1 0.18.0 0.17.7 r460 r458 r455 0.17.3 0.16.1 0.16.0 0.15.5 0.15.4 0.15.3 0.15.2 0.15.1 0.15 0.14.2 0.14.1 克隆/下载 克隆/下载 HTTPS SSH ...
0: no purging; 1: light; 2/3: aggressive [0 for trio; 3 for unzip] -s FLOAT similarity threshold for duplicate haplotigs [0.75 for -l1/-l2, 0.55 for -l3] -O INT min number of overlapped reads for duplicate haplotigs [1] --purge-cov INT coverage upper bound of Purge-dups [...
-r Rounds of haplotype-aware error corrections [3]. This option affects all outputs of hifiasm\_meta. --min-hist-cnt When analyzing the k-mer spectrum, ignore counts below INT [5]. # Assembly options -z Length of adapters that should be removed [0]. This option remove INT bases from...
Purge_Dups.cpp Purge_Dups.h README.md Trio.cpp anchor.cpp code_of_conduct.md extract.cpp gchain_map.cpp gchain_map.h gfa_ut.cpp gfa_ut.h hic.cpp hic.h hifiasm.1 hist.cpp horder.cpp horder.h htab.cpp htab.h inter.cpp inter.h kalloc.cpp kalloc.h kavl.h kdq.h ketopt.h ...
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads - hifiasm/horder.cpp at master · martin-g/hifiasm
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Overlaps_hamt.h POA.cpp POA.h Process_Read.cpp Process_Read.h Purge_Dups.cpp Purge_Dups.h README.md README_ha.md Trio.cpp anchor.cpp data.c extract.cpp gitcommit.h hifiasm.1 hifiasm_meta.1 hist.cpp htab.cpp htab.h kdq.h ketopt.h khashl.h kseq.h ksort.h ksw2.h ksw2_ex...