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r852 -> hybrid correction
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chhylp123
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Hifiasm
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=======
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.. toctree::
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:hidden:
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pa-assembly
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trio-assembly
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hic-assembly
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interpreting-output
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faq
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parameter-reference
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`Hifiasm <https://github.com/chhylp123/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.
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Publications
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============
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Hifiasm
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Haoyu Cheng, Gregory T. Concepcion, Xiaowen Feng, Haowen Zhang & Heng Li.
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`Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm <https://doi.org/10.1038/s41592-020-01056-5>`_. Nature Methods. (2021).
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Install
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=======
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The easiest way to get started is to download a `release <https://github.com/chhylp123/hifiasm/releases>`_. Please report any issues on `github issues <https://github.com/chhylp123/hifiasm/issues>`_ page.
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In addition, the latest unreleased version can be found from github:
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::
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git clone https://github.com/chhylp123/hifiasm
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cd hifiasm && make
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Another way is to install hifiasm via `bioconda <https://anaconda.org/bioconda/hifiasm>`_:
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::
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conda install -c bioconda hifiasm
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Assembly Concepts
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=================
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There are different types of assemblies which are commonly used in practice (see
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`details <https://lh3.github.io/2021/04/17/concepts-in-phased-assemblies>`_).
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Hifiasm produces primary/alternate assemblies or partially phased assemblies
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only with HiFi reads. Given Hi-C data or trio-binning data, hifiasm produces
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contiguous fully-phased assemblies, i.e. haplotype-resolved assemblies.
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Why Hifiasm?
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============
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* Hifiasm delivers high-quality assemblies. It tends to generate longer contigs
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and resolve more segmental duplications than other assemblers.
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* Given Hi-C reads or short reads from the parents, hifiasm can produce overall the best
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haplotype-resolved assembly so far. It is the assembler of choice by the
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`Human Pangenome Project <https://humanpangenome.org/>`_ for the first batch of samples.
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* Hifiasm can purge duplications between haplotigs without relying on
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third-party tools such as purge\_dups. Hifiasm does not need polishing tools
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like pilon or racon, either. This simplifies the assembly pipeline and saves
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running time.
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* Hifiasm is fast. It can assemble a human genome in half a day and assemble a
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~30Gb redwood genome in three days. No genome is too large for hifiasm.
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* Hifiasm is trivial to install and easy to use. It does not required Python,
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R or C++11 compilers, and can be compiled into a single executable. The
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default setting works well with a variety of genomes.
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Learn
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=====
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* :ref:`HiFi-only Assembly <pa-assembly>` - Assembling HiFi reads without additional data types
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* :ref:`Trio-binning Assembly <trio-assembly>` - Producing fully phased assemblies with HiFi and trio-binning data
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* :ref:`Hi-C Integrated Assembly <hic-assembly>` - Producing fully phased assemblies with HiFi and Hi-C data
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* :ref:`Hifiasm Output <interpreting-output>` - Interpreting results
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* :ref:`Hifiasm FAQ <faq>` - Frequently asked questions
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* :ref:`Hifiasm Parameters <parameter-reference>` - Parameter reference of hifiasm
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Hifiasm
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=======
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.. toctree::
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:hidden:
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pa-assembly
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trio-assembly
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hic-assembly
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interpreting-output
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faq
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parameter-reference
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`Hifiasm <https://github.com/chhylp123/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.
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Publications
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============
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Hifiasm
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Haoyu Cheng, Gregory T. Concepcion, Xiaowen Feng, Haowen Zhang & Heng Li.
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`Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm <https://doi.org/10.1038/s41592-020-01056-5>`_. Nature Methods. (2021).
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Install
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=======
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The easiest way to get started is to download a `release <https://github.com/chhylp123/hifiasm/releases>`_. Please report any issues on `github issues <https://github.com/chhylp123/hifiasm/issues>`_ page.
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In addition, the latest unreleased version can be found from github:
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::
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git clone https://github.com/chhylp123/hifiasm
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cd hifiasm && make
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Another way is to install hifiasm via `bioconda <https://anaconda.org/bioconda/hifiasm>`_:
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::
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conda install -c bioconda hifiasm
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Assembly Concepts
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=================
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There are different types of assemblies which are commonly used in practice (see
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`details <https://lh3.github.io/2021/04/17/concepts-in-phased-assemblies>`_).
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Hifiasm produces primary/alternate assemblies or partially phased assemblies
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only with HiFi reads. Given Hi-C data or trio-binning data, hifiasm produces
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contiguous fully-phased assemblies, i.e. haplotype-resolved assemblies.
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Why Hifiasm?
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============
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* Hifiasm delivers high-quality assemblies. It tends to generate longer contigs
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and resolve more segmental duplications than other assemblers.
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* Given Hi-C reads or short reads from the parents, hifiasm can produce overall the best
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haplotype-resolved assembly so far. It is the assembler of choice by the
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`Human Pangenome Project <https://humanpangenome.org/>`_ for the first batch of samples.
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* Hifiasm can purge duplications between haplotigs without relying on
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third-party tools such as purge\_dups. Hifiasm does not need polishing tools
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like pilon or racon, either. This simplifies the assembly pipeline and saves
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running time.
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* Hifiasm is fast. It can assemble a human genome in half a day and assemble a
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~30Gb redwood genome in three days. No genome is too large for hifiasm.
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* Hifiasm is trivial to install and easy to use. It does not required Python,
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R or C++11 compilers, and can be compiled into a single executable. The
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default setting works well with a variety of genomes.
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Learn
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=====
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* :ref:`HiFi-only Assembly <pa-assembly>` - Assembling HiFi reads without additional data types
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* :ref:`Trio-binning Assembly <trio-assembly>` - Producing fully phased assemblies with HiFi and trio-binning data
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* :ref:`Hi-C Integrated Assembly <hic-assembly>` - Producing fully phased assemblies with HiFi and Hi-C data
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* :ref:`Hifiasm Output <interpreting-output>` - Interpreting results
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* :ref:`Hifiasm FAQ <faq>` - Frequently asked questions
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* :ref:`Hifiasm Parameters <parameter-reference>` - Parameter reference of hifiasm
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