Reference based genome assembly

[Jayakumar S]

Hi,
I am going to have the paired end reads from Illumina as well from Pac-bio for genome of about 3 gb.
Can anyone suggest various tools for the reference based genome assembly?
Kindly suggest how should i proceed?

Thanks
Jayakumar S

[Gopo]

Suggestions would depend on many factors such as how closely-related the reference is your current genome. See https://www.biostars.org/p/341670/#347747 for some suggestions. I have had good results with RAGOUT (http://fenderglass.github.io/Ragout/usage.html).

[Jayakumar S]

Thank you for your response and suggestions. They are closely related species but vary in their chromosome number. My idea is to go for reference guided donovo assembly. Kindly suggest about the various tools for the same. Ragout 2 handles large complex genomes.