comparing sets of contigs

Question

[dp]

Hi all

I want to compare contigs assembled from two metagenomic samples that I expect to be similar. For each contig in one of the assemblies I would like to find any contig(s) in the other that it matches and vice versa. I tried building a BLAST db of one and then using blastn to query for the contigs in the other. I find very few matches between the two - I suppose this is possible, but it is very surprising. Is it possible that there are matches and BLAST isn't the best way to find them? Are there other tools that are better suited for this task?

Thanks!

[Joe]

I'd maybe consider using something like CD-HIT instead, to cluster your contigs from both samples. If the contig headers have some identifying info for which file they're from, you should be able to see whether they are grouped with sequences from different metagenomes