Question: minimum contig size in partial eukaryotic assembly
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gravatar for goatsrunfaster
8 months ago by
goatsrunfaster20 wrote:

I have a eukaryotic genome assembly with a lot of smaller contigs (many in the 150bp range). I would like to remove smaller contigs but wasn't sure of the appropriate size. That being said what is the norm in terms of small contig removal for eukaryotic genomes? Note that this is only a partial assembly based on GBS data I'm hoping to map back too, so I'd like to keep as many contigs as possible without risking problematic results.

assembly genome • 139 views
ADD COMMENTlink modified 8 months ago by JC12k • written 8 months ago by goatsrunfaster20
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gravatar for JC
8 months ago by
JC12k
Mexico
JC12k wrote:

what is the norm in terms of small contig removal for eukaryotic genomes?

In many cases you can remove anything smaller than 2 times your read size, some assemblers filter this automatically or set a fixed value (<200bp).

this is only a partial assembly based on GBS data I'm hoping to map back too

then maybe you don't need to remove them, depends on the analysis you want to perform

ADD COMMENTlink written 8 months ago by JC12k
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