Contigs filtering by length in shotgun sequencing data
Hi all!
I was wondering what filtering parameters do you use for filtering you contigs after assembly? I have been trying to find some sort of agreement on how much to filter but it seems its not really standardised. I have high fragmentation (which I expected considering my samples come from soil), and my QUAST shows my N50 is around 1500bp, L50 400000 contigs and auN around 7000. (This is for my MEGAHIT co-asssembly).
I decided to go for 2000bp length filtering as from what I was reading, contigs below 1000bp are likely artifacts/low quality. However, this leaves me with around 4-5% of the total contigs (and about 25-28% of the bases). I am really torn here as I don't know whether these numbers make sense and this is expected/normal, or if I should relax the filtering.
Thanks!