This is a test version of Biostars. For the public version, visit https://www.biostars.org.
optimize post Spades assemblies

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?

assembly assembly genome next-gen
• 1,130 views • link
updated by JC JC • written by zion22 zion22

1 answer

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.

• 0 views • link
written by JC JC

Log in to answer this question.

More posts like this