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Dmitry-Antipov authored Aug 21, 2024
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Expand Up @@ -130,13 +130,13 @@ Hi-C/PoreC integration was tested mostly on human and primate genomes. Please se

### Scaffolding:
Verkko includes a separate scaffolding module which is used when Hi-C or Pore-C data are provided (this is separate from Rukki's ability to connect some contigs into scaffolds with just trio)
Verkko tries to makes a rough estimate of the gap size based on the assembly graph. When the gap size estimate is smaller than 100K we report the estimated value. For larger gaps or gaps were a size cannot be estimated, we always report 100K N's.
Verkko tries to makes a rough estimate of the gap size based on the assembly graph. When the gap size estimate is smaller than 100K we report the estimated value. For larger gaps or gaps where a size cannot be estimated, we always report 100K N's.

The scaffolding module uses telomere positions in the assembly (detected with `seqtk telo`), so if your species has a different telomeric repeat motif than vertebrates (CCCTAA), provide it with the `--telomere-motif` option.

If available, you can provide the genome of another individual of the same or closely related species with the `--ref` option. It is _not_ reference-based assembly; the reference will be only used as guidance in scaffolding.

Since the ccaffolding module relies on the diploid structure of an assembly, it is not compatible with the `--haploid` option; we recommend the [YaHS](https://github.com/c-zhou/yahs) standalone scaffolder for such cases.
Since the scaffolding module relies on the diploid structure of an assembly, it is not compatible with the `--haploid` option; we recommend the [YaHS](https://github.com/c-zhou/yahs) standalone scaffolder for such cases.

Polyploid scaffolding and phasing is not supported yet.

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