This is a test version of Biostars. For the public version, visit https://www.biostars.org.
minimum contig size in partial eukaryotic assembly

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
• 1,133 views • link
updated by JC JC • written by goatsrunfaster • goatsrunfaster

1 answer

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

• 0 views • link
written by JC JC

Log in to answer this question.

More posts like this