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yeeus / GCI

A program for assessing the T2T genome continuity
MIT License
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Why not use illumina reads? #2

Closed zhangwenda0518 closed 9 months ago

zhangwenda0518 commented 9 months ago

Useful tool, I have a question: why not use the common illumina reads, could you add this function?

thanks！

yeeus commented 9 months ago

There are some reasons why not use illumina short reads for detecting issues:

  1. In this T2T era, we have turned to third-generation sequencing from NGS for genome assembly. NGS reads have little effects on improving the continuity of genomes and therefore I don't include illumina reads in this tool.
  2. Due to the short length, mapping of illumina reads usually has more errors than NGS reads, which can be seen when comparing the impacts of HiFi and ONT on GCI (in the table of README) and that would be discussed in the forthcoming paper.
  3. Based on above reasons, detected issues using illumina short reads would be numberless and this is meaningless in a way.