hifiasm

Getting Started

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The second command line will run much faster than the first.

Ultra-long ONT integration

Hifiasm could integrate ultra-long ONT reads to produce the telomere-to-telomere assembly:

hifiasm -o NA12878.asm -t32 --ul ul.fq.gz HiFi-reads.fq.gz

For the single-sample telomere-to-telomere assembly with Hi-C reads:

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:

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.

hifiasm -o NA12878.asm -t32 --dual-scaf HiFi-reads.fq.gz

Preserve more telomeres for T2T assemblies

Hifiasm can preserve more telomeres by specifying the telomere motif using the --telo-m option. Below is an example applied to human genome assembly.

hifiasm -o NA12878.asm -t32 --telo-m CCCTAA HiFi-reads.fq.gz

Output files

Hifiasm generates different types of assemblies based on the input data. It also writes error corrected reads to the prefix.ec.bin binary file and writes overlaps to prefix.ovlp.source.bin and prefix.ovlp.reverse.bin. For more details, please see the complete documentation.

Results

The following table shows the statistics of several hifiasm primary assemblies assembled with v0.12:

Dataset	Size	Cov.	Asm options	CPU time	Wall time	RAM	N50
Mouse (C57/BL6J)	2.6Gb	×25	-t48 -l0	172.9h	4.8h	76G	21.1Mb
Maize (B73)	2.2Gb	×22	-t48 -l0	203.2h	5.1h	68G	36.7Mb
Strawberry	0.8Gb	×36	-t48 -D10	152.7h	3.7h	91G	17.8Mb
Frog	9.5Gb	×29	-t48	2834.3h	69.0h	463G	9.3Mb
Redwood	35.6Gb	×28	-t80	3890.3h	65.5h	699G	5.4Mb
Human (CHM13)	3.1Gb	×32	-t48 -l0	310.7h	8.2h	114G	88.9Mb
Human (HG00733)	3.1Gb	×33	-t48	269.1h	6.9h	135G	69.9Mb
Human (HG002)	3.1Gb	×36	-t48	305.4h	7.7h	137G	98.7Mb

Hifiasm can assemble a 3.1Gb human genome in several hours or a ~30Gb hexaploid redwood genome in a few days on a single machine. For trio binning assembly:

Dataset	Cov.	CPU time	Elapsed time	RAM	N50
HG00733, [father], [mother]	×33	269.1h	6.9h	135G	35.1Mb (paternal), 34.9Mb (maternal)
HG002, [father], [mother]	×36	305.4h	7.7h	137G	41.0Mb (paternal), 40.8Mb (maternal)

Human assemblies above can be acquired from Zenodo and non-human ones are available here.

Getting Help

For detailed description of options, please see tutorial or man ./hifiasm.1. The -h option of hifiasm also provides brief description of options. If you have further questions, please raise an issue at the issue page.

Limitations

1. Purging haplotig duplications may introduce misassemblies.

Citating Hifiasm

If you use hifiasm in your work, please cite:

Cheng, H., Concepcion, G.T., Feng, X., Zhang, H., Li H. (2021) Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods, 18:170-175. https://doi.org/10.1038/s41592-020-01056-5

Cheng, H., Jarvis, E.D., Fedrigo, O., Koepfli, K.P., Urban, L., Gemmell, N.J., Li, H. (2022) Haplotype-resolved assembly of diploid genomes without parental data. Nature Biotechnology, 40:1332–1335. https://doi.org/10.1038/s41587-022-01261-x

Cheng, H., Asri, M., Lucas, J., Koren, S., Li, H. (2024) Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nat Methods, 21:967-970. https://doi.org/10.1038/s41592-024-02269-8