My work involves searching for marker genes/fragments in metagenomic databases (like the Sequence Read Archive). Once I find these sequences, I would like to know more about the neighboring genomic region.
Is there a way I could assemble only sequences that create a contig which contains my region of interest? Contigs which don't contain this region are not useful to me. My organism of interest might represent a minority of the metagenome, and assembling everything in the dataset would use a lot of computing power.