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@@ -164,7 +164,7 @@ For the single-sample telomere-to-telomere assembly with Hi-C reads:
```sh ```sh
hifiasm -o NA12878.asm -t32 --ul ul.fq.gz --h1 read1.fq.gz --h2 read2.fq.gz HiFi-reads.fq.gz hifiasm -o NA12878.asm -t32 --ul ul.fq.gz --h1 read1.fq.gz --h2 read2.fq.gz HiFi-reads.fq.gz
``` ```
For the trio-binning telomere-to-telomere assembly； For the trio-binning telomere-to-telomere assembly:
```sh ```sh
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
``` ```
@@ -174,7 +174,7 @@ hifiasm -o NA12878.asm -t32 --ul ul.fq.gz -1 pat.yak -2 mat.yak HiFi-reads.fq.gz
For diploid haplotype-resolved genome assembly, hifiasm can further enhance assembly contiguity 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. 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 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: homologous region in haplotype 2 to scaffold haplotype 1. Below is an example using the `--dual-scaf` option.
```sh ```sh
hifiasm -o NA12878.asm -t32 --dual-scaf HiFi-reads.fq.gz hifiasm -o NA12878.asm -t32 --dual-scaf HiFi-reads.fq.gz
``` ```