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chhylp123
2025-01-31 20:34:12 -05:00
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@@ -48,6 +48,7 @@ See [tutorial][tutorial] for more details.
- [Why Hifiasm?](#why) - [Why Hifiasm?](#why)
- [Usage](#use) - [Usage](#use)
- [Assembling HiFi reads without additional data types](#hifionly) - [Assembling HiFi reads without additional data types](#hifionly)
- [Assembling ONT reads](#ontonly)
- [Hi-C integration](#hic) - [Hi-C integration](#hic)
- [Trio binning](#trio) - [Trio binning](#trio)
- [Ultra-long ONT integration](#ul) - [Ultra-long ONT integration](#ul)
@@ -119,6 +120,16 @@ bloom filter which takes 16GB memory at the beginning. For genomes much larger
than human, applying `-f38` or even `-f39` is preferred to save memory on k-mer than human, applying `-f38` or even `-f39` is preferred to save memory on k-mer
counting. 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 ### <a name="hic"></a>Hi-C integration
Hifiasm can generate a pair of haplotype-resolved assemblies with paired-end Hifiasm can generate a pair of haplotype-resolved assemblies with paired-end