hifiasm

```sh

git clone https://github.com/chhylp123/hifiasm

cd hifiasm && make

wget https://github.com/chhylp123/hifiasm/releases/download/v0.7/chr11-2M.fa.gz

./hifiasm -o test -t4 -f0 chr11-2M.fa.gz 2> test.log

awk '/^S/{print ">"$2;print $3}' test.bp.p_ctg.gfa > test.p_ctg.fa # get primary contigs in FASTA

hifiasm -o CHM13.asm -t32 -l0 CHM13-HiFi.fa.gz 2> CHM13.asm.log

hifiasm -o HG002.asm -t32 HG002-file1.fq.gz HG002-file2.fq.gz

hifiasm -o HG002.asm --ont -t32 HG002-ont.fq.gz

hifiasm -o HG002.asm --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz

yak count -b37 -t16 -o pat.yak <(cat pat_1.fq.gz pat_2.fq.gz) <(cat pat_1.fq.gz pat_2.fq.gz)

yak count -b37 -t16 -o mat.yak <(cat mat_1.fq.gz mat_2.fq.gz) <(cat mat_1.fq.gz mat_2.fq.gz)

hifiasm -o HG002.asm -t32 -1 pat.yak -2 mat.yak HG002-HiFi.fa.gz

hifiasm -o HG002.asm --dual-scaf --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz

hifiasm -o HG002.asm --telo-m CCCTAA --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz

hifiasm -o HG002.asm --h1 read1.fq.gz --h2 read2.fq.gz --ul ul.fq.gz HG002-HiFi.fq.gz

hifiasm -o HG002.asm --dual-scaf --telo-m CCCTAA --h1 read1.fq.gz --h2 read2.fq.gz --ul ul.fq.gz HG002-HiFi.fq.gz

```

See [tutorial][tutorial] for more details.

• [Getting Started](#started)
• [Introduction](#intro)
• [Why Hifiasm?](#why)
• [Usage](#use)
• [Assembling HiFi reads without additional data types](#hifionly)
• [Assembling ONT reads](#ontonly)
• [Hi-C integration](#hic)
• [Trio binning](#trio)
• [Ultra-long ONT integration](#ul)
• [Output files](#output)
• [Results](#results)
• [Getting Help](#help)
• [Limitations](#limit)
• [Citing Hifiasm](#cite)

Hifiasm is a fast haplotype-resolved de novo assembler initially designed for PacBio HiFi reads.

Its latest release could support the telomere-to-telomere assembly by utilizing ultralong Oxford Nanopore reads. Hifiasm produces arguably the best single-sample telomere-to-telomere assemblies combing HiFi, ultralong and Hi-C reads, and it is one of the best haplotype-resolved assemblers for the trio-binning assembly given parental short reads. For a human genome, hifiasm can produce the telomere-to-telomere assembly in one day.

• Hifiasm delivers high-quality telomere-to-telomere 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][hpp] 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.

[hpp]: https://humanpangenome.org

A typical hifiasm command line looks like:

```sh

hifiasm -o NA12878.asm -t 32 NA12878.fq.gz

```

where NA12878.fq.gz provides the input reads, -t sets the number of CPUs in

use and -o specifies the prefix of output files. For this example, the

primary contigs are written to NA12878.asm.bp.p_ctg.gfa.

Since v0.15, hifiasm also produces two sets of

partially phased contigs at NA12878.asm.bp.hap?.p_ctg.gfa. This pair of files

can be thought to represent the two haplotypes in a diploid genome, though with

occasional switch errors. The frequency of switches is determined by the

heterozygosity of the input sample.

At the first run, hifiasm saves corrected reads and

overlaps to disk as NA12878.asm.*.bin. It reuses the saved results to avoid

the time-consuming all-vs-all overlap calculation next time. You may specify

-i to ignore precomputed overlaps and redo overlapping from raw reads.

You can also dump error corrected reads in FASTA and read overlaps in PAF with

```sh

hifiasm -o NA12878.asm -t 32 --write-paf --write-ec /dev/null

```

Hifiasm purges haplotig duplications by default. For inbred or homozygous

genomes, you may disable purging with option -l0. Old HiFi reads may contain

short adapter sequences at the ends of reads. You can specify -z20 to trim

both ends of reads by 20bp. For small genomes, use -f0 to disable the initial

bloom filter which takes 16GB memory at the beginning. For genomes much larger

than human, applying -f38 or even -f39 is preferred to save memory on k-mer

counting.

Since version 0.21.0 (r686), hifiasm can support ONT assembly using ONT simplex R10 reads.

To enable this feature, add the --ont option as shown below:

```sh

hifiasm -t64 --ont -o ONT.asm ONT.read.fastq.gz

```

Please note that this module requires input reads in FASTQ format.