diff --git a/README.md b/README.md index 75a556d..f879814 100644 --- a/README.md +++ b/README.md @@ -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 ``` +### 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 +``` + ### Output files Hifiasm generates different types of assemblies based on the input data.