Is there a way to assemble contigs starting from a specific sequence? 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.
This is one of the primary use cases for which spacegraphcats (preprint and code) was designed. The "neighborhood queries" discussed in the paper sound particularly relevant. I don't have any personal experience with spacegraphcats, but the run guide provides some examples of how to index the complete data set and how to query sequences of interest.