Question: Existing Tools For Building A De Bruijn Graph From Raw Reads
2
gravatar for Tianyang Li
6.4 years ago by
Tianyang Li490
Beijing, China
Tianyang Li490 wrote:

Hi,

I'm wondering if there are any existing tools for building a de Bruijn graph from raw reads?

I have some doubts about current de novo assemblers, so I'd like to go to a lower level and directly use de Bruijn graphs. But apparently there doesn't seem to be existing tools for doing this.

Thanks!

ADD COMMENTlink written 6.4 years ago by Tianyang Li490
3
gravatar for Dan D
6.4 years ago by
Dan D6.6k
Tennessee
Dan D6.6k wrote:

The Trinity tool for RNA-Seq has a component called "Chrysalis" that generates deBruijn graphs. If you visit the link I provided, you can see how to run Chrysalis in isolation, which may give you what you want. Digging deeper, there's a dedicated tool used by Chrysalis called FastaToDeBruijn that might be exactly what you're looking for. I've never run that specific tool in isolation, but given what i know about the Trinity toolset and how it's assembled, I bet if you picked through the source you could adapt it to work with non-RNAseq data.

I'm actually pretty interested to see what you come up with. Keep me posted because I might like to join in if you run into difficulties.

ADD COMMENTlink written 6.4 years ago by Dan D6.6k

There's a file called LastGraph in Velvet's output. You can read more about it in the manual. But I'll email Trinity's authors and see what's available from Trinity.

ADD REPLYlink written 6.4 years ago by Tianyang Li490

You can see the link in my answer.

ADD REPLYlink written 6.4 years ago by Tianyang Li490

Awesome, thanks for the update and I'm glad you found what you needed.

ADD REPLYlink written 6.4 years ago by Dan D6.6k
3
gravatar for erwan.scaon
6.4 years ago by
erwan.scaon580
Limoges - CBRS - France
erwan.scaon580 wrote:

A software that constructs the de Bruijn graph is part of the KisSplice package, it can be found here : https://github.com/rchikhi/debruijn

ADD COMMENTlink written 6.4 years ago by erwan.scaon580

Are there any other tools that you are aware of?

ADD REPLYlink written 6.4 years ago by Tianyang Li490
0
gravatar for Tianyang Li
6.4 years ago by
Tianyang Li490
Beijing, China
Tianyang Li490 wrote:

Trinity can do this. See this messsage.

ADD COMMENTlink written 6.4 years ago by Tianyang Li490
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