Existing Tools For Building A De Bruijn Graph From Raw Reads

Question

[Tianyang Li]

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!

Answer 1

[Dan D]

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.

[Tianyang Li]

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.

[Tianyang Li]

You can see the link in my answer.

[Dan D]

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

Answer 2

[erwan.scaon]

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

[Tianyang Li]

Are there any other tools that you are aware of?

Answer 3

[Tianyang Li]

Trinity can do this. See this messsage.