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README.md
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## Getting Started
## <a name="started"></a>Getting Started
```sh
# Install hifiasm (requiring g++ and zlib)
@@ -19,23 +19,40 @@ hifiasm -o HG002.asm -t32 HG002-file1.fq.gz HG002-file2.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
# Hi-C phasing with paired-end short reads in two FASTQ files
hifiasm -o HG002.asm --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz
```
## Introduction
## Table of Contents
Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads.
It can assemble a human genome in several hours and works with the California
redwood genome, one of the most complex genomes sequenced so far. Hifiasm can
produce primary/alternate assemblies of quality competitive with the best
assemblers. It also introduces a new graph binning algorithm and achieves
the best haplotype-resolved assembly given trio data.
- [Getting Started](#started)
- [Introduction](#intro)
- [Why Hifiasm?](#why)
- [Usage](#use)
- [Assembling HiFi reads without additional data types](#hifionly)
- [Hi-C integration](#hic)
- [Trio binning](#trio)
- [Output files](#output)
- [Results](#results)
- [Getting Help](#help)
- [Limitations](#limit)
- [Citing Hifiasm](#cite)
## Why Hifiasm?
## <a name="intro"></a>Introduction
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.
## <a name="why"></a>Why Hifiasm?
* Hifiasm delivers high-quality assemblies. It tends to generate longer contigs
and resolve more segmental duplications than other assemblers.
* Given sequence reads from the parents, hifiasm can produce overall the best
* 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.
@@ -47,13 +64,15 @@ the best haplotype-resolved assembly given trio data.
* 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
* 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
## Usage
## <a name="use"></a>Usage
### <a name="hifionly"></a>Assembling HiFi reads without additional data types
A typical hifiasm command line looks like:
```sh
@@ -61,11 +80,21 @@ 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.p_ctg.gfa` and alternate contigs to
`NA12878.asm.a_ctg.gfa`. At the first run, hifiasm saves corrected reads and
primary contigs are written to `NA12878.asm.bp.p_ctg.gfa` and alternate contigs to
`NA12878.asm.bp.a_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 in FASTA and/or 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
@@ -75,7 +104,24 @@ 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.
When parental short reads are available, hifiasm can generate a pair of
### <a name="hic"></a>Hi-C integration
Hifiasm can generate a pair of haplotype-resolved assemblies with paired-end
Hi-C reads:
```sh
hifiasm -o NA12878.asm -t32 --h1 read1.fq.gz --h2 read2.fq.gz HiFi-reads.fq.gz
```
In this mode, each contig is supposed to be a haplotig, which by definition
comes from one parental haplotype only. Hifiasm often puts all contigs from the
same parental chromosome in one assembly. It has cleanly separated chrX and
chrY for a human male dataset. Nonetheless, phasing across centromeres is
challenging. Users should not expect hifiasm to phase entire chromosomes at the
moment. Also, contigs from different parental chromosomes are randomly mixed as
it is just not possible to phase across chromosomes with Hi-C.
### <a name="trio"></a>Trio binning
When parental short reads are available, hifiasm can also generate a pair of
haplotype-resolved assemblies with trio binning. To perform such assembly, you
need to count k-mers first with [yak][yak] first and then do assembly:
```sh
@@ -85,19 +131,15 @@ hifiasm -o NA12878.asm -t 32 -1 pat.yak -2 mat.yak NA12878.fq.gz
```
Here `NA12878.asm.hap1.p_ctg.gfa` and `NA12878.asm.hap2.p_ctg.gfa` give the two
haplotype assemblies. In the binning mode, hifiasm does not purge haplotig
duplications by default. Because hifiasm reuses saved overlaps, you can
duplicates by default. Because hifiasm reuses saved overlaps, you can
generate both primary/alternate assemblies and trio binning assemblies with
```sh
hifiasm -o NA12878.asm -t 32 NA12878.fq.gz 2> NA12878.asm.pri.log
hifiasm -o NA12878.asm -t 32 -1 pat.yak -2 mat.yak /dev/null 2> NA12878.asm.trio.log
```
The second command line will run much faster than the first. You can also dump
error corrected in FASTA and/or overlaps in PAF with
```sh
hifiasm -o NA12878.asm -t 32 --write-paf --write-ec /dev/null
```
The second command line will run much faster than the first.
## Output files
### <a name="output"></a>Output files
For non-trio assembly, hifiasm generates the following files:
@@ -126,9 +168,9 @@ For trio assembly, hifiasm generates the following files:
Hifiasm writes error corrected reads to the *prefix*.ec.bin binary file and
writes overlaps to *prefix*.ovlp.source.bin and *prefix*.ovlp.reverse.bin.
## Results
## <a name="results"></a>Results
The following table shows the statistics of several hifiasm primary assemblies:
The following table shows the statistics of several hifiasm primary assemblies assembled with v0.12:
|<sub>Dataset<sub>|<sub>Size<sub>|<sub>Cov.<sub>|<sub>Asm options<sub>|<sub>CPU time<sub>|<sub>Wall time<sub>|<sub>RAM<sub>|<sub> N50<sub>|
|:---------------|-----:|-----:|:---------------------|-------:|--------:|----:|----------------:|
@@ -155,7 +197,10 @@ redwood genome in a few days on a single machine. For trio binning assembly:
|:---------------|-----:|-------:|--------:|----:|----------------:|
|<sub>[HG00733][HG00733-data], [\[father\]][HG00731-data], [\[mother\]][HG00732-data]</sub>|<sub>&times;33</sub>|<sub>269.1h</sub>|<sub>6.9h</sub>|<sub>135G</sub>|<sub>35.1Mb (paternal), 34.9Mb (maternal)</sub>|
|<sub>[HG002][NA24385-data], [\[father\]][NA24149-data], [\[mother\]][NA24143-data]</sup>|<sub>&times;36</sub>|<sub>305.4h</sub>|<sub>7.7h</sub>|<sub>137G</sub>|<sub>41.0Mb (paternal), 40.8Mb (maternal)</sub>|
<!--
|<sub>[NA12878][NA12878-data], [\[father\]][NA12891-data], [\[mother\]][NA12892-data]</sub>|<sub>&times;30</sub>|<sub>180.8h</sub>|<sub>4.9h</sub>|<sub>123G</sub>|<sub>27.7Mb (paternal), 27.0Mb (maternal)</sub>|
-->
[HG00733-data]: https://www.ebi.ac.uk/ena/data/view/ERX3831682
[HG00731-data]: https://www.ebi.ac.uk/ena/data/view/ERR3241754
@@ -167,33 +212,32 @@ redwood genome in a few days on a single machine. For trio binning assembly:
[NA12891-data]: https://www.ebi.ac.uk/ena/data/view/ERR194160
[NA12892-data]: https://www.ebi.ac.uk/ena/data/view/ERR194161
Except NA12878, the assemblies above were produced by hifiasm v0.12 and can be
downloaded at
```txt
ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/submission/hifiasm-0.12/
```
NA12878 was assembled with an older version of hifiasm and is available at
```txt
ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/NA12878-r253/
```
Human assemblies above can be acquired [from Zenodo][zenodo-human] and
non-human ones are available [here][zenodo-nonh].
[zenodo-human]: https://zenodo.org/record/4393631
[zenodo-nonh]: https://zenodo.org/record/4393750
[unitig]: http://wgs-assembler.sourceforge.net/wiki/index.php/Celera_Assembler_Terminology
[gfa]: https://github.com/pmelsted/GFA-spec/blob/master/GFA-spec.md
[paf]: https://github.com/lh3/miniasm/blob/master/PAF.md
[yak]: https://github.com/lh3/yak
## Getting Help
## <a name="help"></a>Getting Help
For detailed description of options, please see `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](https://github.com/chhylp123/hifiasm/issues).
## Limitations
## <a name="limit"></a>Limitations
1. Purging haplotig duplications may introduce misassemblies.
## Citation
## <a name="cite"></a>Citating Hifiasm
Cheng, H., Concepcion, G.T., Feng, X., Zhang, H., Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 18, 170–175 (2021). https://doi.org/10.1038/s41592-020-01056-5
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