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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.

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  • $\begingroup$ Good question! I know that some of the assemblers for mtDNA are working on this principle - searching for reads mapping to a conserved mt gene and then extending the sequence, maybe you could tweak one of those tools. $\endgroup$ Commented Apr 9, 2019 at 11:57

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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.

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    $\begingroup$ Yes, we'd be happy to chat (I'm one of the spacegraphcats authors). Just post questions over on our github repo! $\endgroup$ Commented Apr 9, 2019 at 17:58
  • $\begingroup$ You might also be interested in citations 21 and 22 in the spacegraphcats paper - metacherchant and a paper that does something similar. $\endgroup$ Commented Apr 9, 2019 at 17:58

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