xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-29 03:08:13 +08:00
Code Issues Packages Projects Releases Wiki Activity

fix conflict

Browse Source
This commit is contained in:
chhylp123
2020-10-21 22:01:07 -04:00
parent 91d4915da7
commit 53adde2b37
1 changed files with 27 additions and 4 deletions
Download Patch File Download Diff File Expand all files Collapse all files
README.md
+27 -4
View File
@@ -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
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
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
[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
```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
ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/NA12878-r253/
```
@@ -169,4 +192,4 @@ page](https://github.com/chhylp123/hifiasm/issues).
## Limitations
1. Purging haplotig duplications may introduce misassemblies.
1. Purging haplotig duplications may introduce misassemblies.