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chhylp123
2020-10-21 22:01:07 -04:00
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@@ -30,6 +30,29 @@ produce primary/alternate assemblies of quality competitive with the best
assemblers. It also introduces a new graph binning algorithm and achieves assemblers. It also introduces a new graph binning algorithm and achieves
the best haplotype-resolved assembly given trio data. the best haplotype-resolved assembly given trio data.
## 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
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
## Usage ## Usage
A typical hifiasm command line looks like: A typical hifiasm command line looks like:
@@ -144,12 +167,12 @@ 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 [NA12891-data]: https://www.ebi.ac.uk/ena/data/view/ERR194160
[NA12892-data]: https://www.ebi.ac.uk/ena/data/view/ERR194161 [NA12892-data]: https://www.ebi.ac.uk/ena/data/view/ERR194161
Except NA12878, the assemblies above were produced by hifiasm v0.7 and can be Except NA12878, the assemblies above were produced by hifiasm v0.12 and can be
downloaded at downloaded at
```txt ```txt
ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/submission/v0.7/ ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/submission/hifiasm-0.12/
``` ```
NA12878 was assembled with a more recent version of hifiasm and is available at NA12878 was assembled with an older version of hifiasm and is available at
```txt ```txt
ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/NA12878-r253/ ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/NA12878-r253/
``` ```