text: user4401: 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.
  
  user96: 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.
  
original_text: 4401: <p>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. </p>
  
  <p>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.</p>
   96: <p>This is one of the primary use cases for which spacegraphcats (<a href="https://www.biorxiv.org/content/10.1101/462788v2" rel="nofollow noreferrer">preprint</a> and <a href="https://github.com/spacegraphcats/spacegraphcats" rel="nofollow noreferrer">code</a>) was designed. The "neighborhood queries" discussed in the paper sound particularly relevant. I don't have any personal experience with spacegraphcats, but the <a href="https://github.com/spacegraphcats/spacegraphcats/blob/master/doc/running-spacegraphcats.md" rel="nofollow noreferrer">run guide</a> provides some examples of how to index the complete data set and how to query sequences of interest.</p>
  