<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>

CC BY-SA 4.0
2019-04-09T17:58:31.013Z
Yes, we'd be happy to chat (I'm one of the spacegraphcats authors). Just post questions over on our github repo!
Titus Brown
CC BY-SA 4.0
2019-04-09T17:58:39.067Z
You might also be interested in citations 21 and 22 in the spacegraphcats paper - metacherchant and a paper that does something similar.
Titus Brown
CC BY-SA 4.0
2019-04-09T16:18:30.580Z
2019-04-09T16:18:30.580Z
Daniel Standage
<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>

CC BY-SA 4.0
2019-04-09T11:57:52.897Z
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.
Kamil S Jaron
<phylogenetics><fasta><assembly><metagenome>
Is there a way to assemble contigs starting from a specific sequence?
# Is there a way to assemble contigs starting from a specific sequence?

(Asked by: username_0 on 2019-04-09)

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.

**Tags:** phylogenetics, fasta, assembly, metagenome
> **Comments:**
> **username_1**: 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.  

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## 1 answers

### Answer by username_2 on 2019-04-09. Score: 2 | Accepted answer

This is one of the primary use cases for which spacegraphcats ([preprint](https://www.biorxiv.org/content/10.1101/462788v2) and [code](https://github.com/spacegraphcats/spacegraphcats)) 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](https://github.com/spacegraphcats/spacegraphcats/blob/master/doc/running-spacegraphcats.md) provides some examples of how to index the complete data set and how to query sequences of interest.

> **Comments:**
> **username_3**: Yes, we'd be happy to chat (I'm one of the spacegraphcats authors). Just post questions over on our github repo!  
> **username_3**: You might also be interested in citations 21 and 22 in the spacegraphcats paper - metacherchant and a paper that does something similar.  

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