optimize post Spades assemblies

Question

[zion22]

Hi I have a question for you, how can I optimize my assemblages of a de novo genome (without any kind of similar genome), since I currently use Spades for this process, but I have noticed that the amount of contings that I generate are many, and I would like to decrease the amount as much as possible, some of you could intrude me a workflow suitable to do this?

Answer 1

[JC]

SPAdes already uses different k-mers sizes in the assembly, you can try to adjust the predefined k-mers, but in general, adding more sequencing data is better, even better if you use a different insert size or larger sequencing reads such as PacBio.