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update readme
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chhylp123 committed Feb 1, 2025
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Expand Up @@ -48,6 +48,7 @@ See [tutorial][tutorial] for more details.
- [Why Hifiasm?](#why)
- [Usage](#use)
- [Assembling HiFi reads without additional data types](#hifionly)
- [Assembling ONT reads](#ontonly)
- [Hi-C integration](#hic)
- [Trio binning](#trio)
- [Ultra-long ONT integration](#ul)
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than human, applying `-f38` or even `-f39` is preferred to save memory on k-mer
counting.

### <a name="ontonly"></a>Assembling ONT reads

Since version 0.21.0 (r686), hifiasm can support ONT assembly using ONT simplex R10 reads.
To enable this feature, add the `--ont` option as shown below:
```sh
hifiasm -t64 --ont -o ONT.asm ONT.read.fastq.gz
```
Please note that this module requires input reads in FASTQ format.


### <a name="hic"></a>Hi-C integration

Hifiasm can generate a pair of haplotype-resolved assemblies with paired-end
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