针对数据：PacBio, ONT
Flye is a de novo assembler for single-molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PacBio / ONT reads as input and outputs polished contigs. Flye also has a special mode for metagenome assembly. Currently, Flye will produce collapsed assemblies of diploid genomes, represented by a single mosaic haplotype. To recover two phased haplotypes consider applying HapDup after the assembly.Flye 用于单分子测序reads的从头组装，如PacBio和ONT的测序reads。适用范围广——从细菌到大型哺乳动物的组装项目。这个包整合了一个完整的pipeline：PacBio/ONT reads作为输入，输出polish后的contigs。Flye也有用于宏基因组组装的特殊模式。
目前，Flye能够产生二倍体基因组的 collapsed 组装，。
针对数据：PacBio (HiFi or CLR), ONT
HapDup (haplotype duplicator) is a pipeline to convert a haploid long read assembly into a diploid assembly. HapDup works with either Oxford Nanopore or PacBio (HiFi or CLR). The reconstructed haplotypes preserve heterozygous structural variants (in addition to small variants) and are locally phased.HapDup 是一个将单倍体长 read 组装转换为 二倍体组装。重建的单倍型保留了杂合子结构变异（除了小变异）和局部分型。
参考
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