minimum contig size in partial eukaryotic assembly

Question

[goatsrunfaster]

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.

Answer 1

[JC]

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