Yeast reference-based genome assembly

Question

[amy967107]

Hello everyone!

I'm trying to perform a reference-based genome assembly using Nanopore sequencing data. The gene originates from yeast, presumably from the genus Rhodotorula, and I currently have two candidate reference genomes that could be used. Could anyone recommend a reference-based assembly pepline or tool suitable for yeast?

I've seen potential tools like LRSDAY, which is best suited for Saccharomyces cerevisiae and may require some adjustments, and RGAAT. Would either of these be suitable? After assembling the gene, I'll need to annotate it and use it for subsequent prediction of functional enzymes.

Thanks in advance for your help!

[GenoMax]

The gene originates from yeast,

What does this mean? Are you putting a gene from a different genus/species into some other yeast? Can you describe the experiment you are doing.

Answer 1

[colindaven]

Nanopore reads are long enough to create a full assembly. Why not first try to create a whole genome assembly with a tool like Flye if you have enough coverage 20x+ ?

Then look for you gene in the assembly contigs using blast etc. Please list your data volume, expected coverage etc or file sizes so we can better help you.