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update README

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chhylp123
2022-11-17 12:26:33 -05:00
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@@ -34,6 +34,7 @@ See [tutorial][tutorial] for more details.
- [Assembling HiFi reads without additional data types](#hifionly) - [Assembling HiFi reads without additional data types](#hifionly)
- [Hi-C integration](#hic) - [Hi-C integration](#hic)
- [Trio binning](#trio) - [Trio binning](#trio)
- [Ultra-long ONT integration](#ul)
- [Output files](#output) - [Output files](#output)
- [Results](#results) - [Results](#results)
- [Getting Help](#help) - [Getting Help](#help)
@@ -143,6 +144,14 @@ hifiasm -o NA12878.asm -t 32 -1 pat.yak -2 mat.yak /dev/null 2> NA12878.asm.trio
``` ```
The second command line will run much faster than the first. The second command line will run much faster than the first.
### <a name="ul"></a>Ultra-long ONT integration
Hifiasm could integrate ultra-long ONT reads to improve the assembly quality:
```sh
hifiasm -o NA12878.asm -t32 --ul ul.fq.gz HiFi-reads.fq.gz
```
Please note that this mode is not stable right now.
### <a name="output"></a>Output files ### <a name="output"></a>Output files
Hifiasm generates different types of assemblies based on the input data. Hifiasm generates different types of assemblies based on the input data.