Hifiasm is a fast haplotype-resolved de novo assembler for PacBio HiFi reads. It can assemble a human genome in several hours and assemble a ~30Gb California redwood genome in a few days. Hifiasm emits partially phased assemblies of quality competitive with the best assemblers. Given parental short reads or Hi-C data, it produces arguably the best haplotype-resolved assemblies so far.
Haoyu Cheng, Gregory T. Concepcion, Xiaowen Feng, Haowen Zhang & Heng Li. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods. (2021).
The easiest way to get started is to download a release. Please report any issues on github issues page.
In addition, the latest unreleased version can be found from github:
git clone https://github.com/chhylp123/hifiasm cd hifiasm && make
Another way is to install hifiasm via bioconda:
conda install -c bioconda hifiasm
There are different types of assemblies which are commonly used in practice (see details). Hifiasm produces primary/alternate assemblies or partially phased assemblies only with HiFi reads. Given Hi-C data or trio-binning data, hifiasm produces contiguous fully-phased assemblies, i.e. haplotype-resolved assemblies.
Hifiasm delivers high-quality assemblies. It tends to generate longer contigs and resolve more segmental duplications than other assemblers.
Given Hi-C reads or short reads from the parents, hifiasm can produce overall the best haplotype-resolved assembly so far. It is the assembler of choice by the Human Pangenome Project for the first batch of samples.
Hifiasm can purge duplications between haplotigs without relying on third-party tools such as purge_dups. Hifiasm does not need polishing tools like pilon or racon, either. This simplifies the assembly pipeline and saves running time.
Hifiasm is fast. It can assemble a human genome in half a day and assemble a ~30Gb redwood genome in three days. No genome is too large for hifiasm.
Hifiasm is trivial to install and easy to use. It does not required Python, R or C++11 compilers, and can be compiled into a single executable. The default setting works well with a variety of genomes.
HiFi-only Assembly - Assembling HiFi reads without additional data types
Trio-binning Assembly - Producing fully phased assemblies with HiFi and trio-binning data
Hi-C Integrated Assembly - Producing fully phased assemblies with HiFi and Hi-C data
Hifiasm Output - Interpreting results
Hifiasm FAQ - Frequently asked questions
Hifiasm Parameters - Parameter reference of hifiasm