hifiasm 会随机选择每个气泡的一边构建primary assembly(与 Falcon-Unzip 和 HiCanu 类似的主装配)。 对于杂合基因组,由于存在一个以上的纯合haplotype,因此primary assembly可能还会包含haplotigs。 HiCanu 依靠第三方工具(如 purge_dups20)来去除多余的haplotigs。Hifiasm 集成实现了 purge_dups 算法的一个变体,简化了...
老师您好。hifiasm初步组装结果比预估大10%,也就是100M。我分别用purge_dup和nextpolish进行了分析。purge_dup直接移除了一个40M的contig。nextpolish把每条大的contig都删去了6-10M左右。两个分析的结果虽然各有优劣,但都还是不理想。可以先用purge_dup去冗余,然后再用nextpolish进行polish吗,或者相反的顺序。1 条评...
Hi I found the hifiasm will purge assembly when use default -l parameter, which got the same hifiasm.p_ctg.fasta as "-l 2". And when I use default parameter to assembly, and the use 'purge_dups' purging , it still purge more. But my coll...
你这个相差太大，是不是基因组survery 做的有问题；多倍体建议用GenomeScope 2.0 评估，GenomeScope 1.0...
{///0: disable purge_dup; 1: purge containment; 2: purge overlap asm_opt->purge_level_primary= asm_opt->purge_level_trio=atoi(opt.arg); Expand Down 3 changes: 2 additions & 1 deletion3CommandLines.h Original file line numberDiff line numberDiff line change ...
(约2300字)1. Hifiasm软件的基本算法Hifiasm软件由哈佛大学李恒团队在2021年2月份发表在Nature Methods上。Hifiasm组装主要分为三步:校正测序错误构建分型字...
HiCanu 依靠第三方工具(如 purge_dups20)来去除多余的haplotigs。Hifiasm 集成实现了 purge_dups 算法的一个变体,简化了组装流程。 2. Hifiasm(trio)算法:Trio-binning模式 如果样本的亲本也进行了测序,则可以使用Trio-binning模式。Trio-binning模式主要在单倍体分型组装步骤上与上面不同。
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{ ///0: disable purge_dup; 1: purge containment; 2: purge overlap asm_opt->purge_level_primary = asm_opt->purge_level_trio = atoi(opt.arg); @@ -520,7 +532,6 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt) Print_H(asm_opt); return 0; } //...