Tool(S) For Post-Velvet Microbial Sequence Assembly/Alignment

Question

[Mat]

Hi,

I have a set of NGS sequences for Staph aureus which I've assembled using Velvet. The assembly is incomplete, and I now need to use comparison to reference sequences to make some sense of what I've generated. What tools prove particularly good for this? I'm pretty much a beginner at this so I look forward to all suggestions

thanks

m

Answer 1

[Nick Loman]

As well as Mummer, I would definitely suggest checking out Mauve which is both a whole-genome aligner (can do multiple genomes) as well as a great alignment viewer.

http://asap.ahabs.wisc.edu/mauve/

[Mat]

thanks Nick; I picked up on Velvet use from your blog comments back in 2009; thanks for that - very useful. M

Answer 2

[Pasta]

The best option for me is to use MUMmer. The inlcuded tools mapview and mummerplot will give you pretty good visualisation of your data.

With mummerplot:

Consequently, with a bit of extra computing work you can also use the output of MUMmer into CIRCOS to have a nice circular representation, like this one below. Believe me, biologists love this kind of representation !

Believe me, biologists love this kind of representation !

[Mat]

nice! thank you, I'll take a look. m