I've run my samples through metaspades and am in the process of cleaning out some contigs that I don't need (i.e. obvious contamination). However I don't see (or maybe I missed) anything in the metaspades guidelines about the minimum length it keeps for contigs. In fact I see many contigs of lengths quite short (<100bp). If my target length was 150bp, should I remove contig lengths less than this or in fact increase the minimum contig length to remove?
If anyone has some good documentation on best practise for this I would greatly appreciate it.