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schneebergerlab / findGSE

findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a skew normal distribution model.
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Can findGSE use third generation sequencing reads？ #7

Closed CSU-KangHu closed 7 months ago

CSU-KangHu commented 3 years ago

I'm using three generations of sequencing reads, and I want to estimate the coverage of the reads (no reference or assembly). Can findGSE use the third-generation sequencing reads and estimate the coverage of the reads?

HeQSun commented 3 years ago

Hi,

Which type of third generation data did you mean?

With nanopore reads, I am not sure because of the high sequencing errors.

If HiFi, I think it's possible to count k-mers, then you can estimate sequencing depth.

Best, Hequan