Question: optimize post Spades assemblies
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gravatar for zion22
19 days ago by
zion2240
merilla
zion2240 wrote:

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?

next-gen assembly genome • 79 views
ADD COMMENTlink modified 19 days ago by JC8.4k • written 19 days ago by zion2240
0
gravatar for JC
19 days ago by
JC8.4k
Mexico
JC8.4k wrote:

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.

ADD COMMENTlink written 19 days ago by JC8.4k
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