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@@ -169,6 +169,16 @@ For the trio-binning telomere-to-telomere assembly；
hifiasm -o NA12878.asm -t32 --ul ul.fq.gz -1 pat.yak -2 mat.yak HiFi-reads.fq.gz hifiasm -o NA12878.asm -t32 --ul ul.fq.gz -1 pat.yak -2 mat.yak HiFi-reads.fq.gz
``` ```
### <a name="ul"></a>Self-scaffolding
For diploid haplotype-resolved genome assembly, hifiasm can further enhance assembly contiguity
by introducing scaffolding. It leverages the assemblies of the two haplotypes to scaffold each other.
Specifically, if there is a gap within the haplotype 1 assembly, hifiasm will use the corresponding
homologous region in haplotype 2 to scaffold haplotype 1. Below is an example using the `--dual-scaf` option:
```sh
hifiasm -o NA12878.asm -t32 --dual-scaf HiFi-reads.fq.gz
```
### <a name="output"></a>Output files ### <a name="output"></a>Output files
Hifiasm generates different types of assemblies based on the input data. Hifiasm generates different types of assemblies based on the input data.