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yilinZhang-bio / Four-rice-gap-free-genome

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Question about the pollish step #1

Open Orz-CQ opened 2 years ago

Orz-CQ commented 2 years ago

Hi, First, I am wondering the step: Finally, the HiFi and short reads were combined to polish the ONT assembly. What software did you use to polish the genome?

Second, what are the sequencing depth of your HIFI data, ONT data and illumina data?

For these information I can not found in the paper, I put my question here. Thanks a lot!

yilinZhang-bio commented 2 years ago
  1. NextPolish (https://github.com/Nextomics/NextPolish/)

In addition, it is recommended that you use the latest polish method. Please refer to this paper and GitHub. Mc Cartney AM, Shafin K, Alonge M et al. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nat Methods (2022) doi: https://doi.org/10.1038/s41592-022-01440-3

https://github.com/arangrhie/T2T-Polish

2.About 50X nanopore ultra-long reads (N50>100K ~17G), Pacbio HiFi reads generated 29G-47G data for XL628S (~87X), LK638S (~73X), J4155S (~120X), and HZ (~102X), and Illumina generated 6-22G paired-end sequencing data respectively.

Best wishes, Yilin