Genome scope for Hybrid assembly

Question

[Sowmya Pulapet]

Hi,

I am going to do a hybrid assembly for a plant using Illumina and Nanopore reads with the help of the MasuRCA tool. Prior to this I would like to run Genomescope.

My doubt is which reads should I use to run Genomescope ? At first I did an assembly using only short reads and for that I had estimated a genome size using Genomescope. So would that value change now that I am doing hybrid assembly ?

Hope someone would help me.

Thank you.

Answer 1

[colindaven]

How big is your plant genome and how much coverage do you have ? Also what is your data quality (Q20 etc, or better percent alignment to a close reference genome ?). Or just pore eg 9.4.1 or 10.4.1 and sequencing date ?

I would use Shasta (if 20-60X) or Flye (if 20X +) depending on genome size, if you have enough coverage.Masurca is older,and slower I believe.

Use the Illumina reads for downstream polishing instead.

[Sowmya Pulapet]

Thank you for you suggestions. Would take these into consideration.