Question

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

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12.7 years ago

Mat ▴ 50

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

velvet assembly • 3.5k views

ADD COMMENT • link updated 12.7 years ago by Nick Loman ▴ 610 • written 12.7 years ago by Mat ▴ 50

score 4 · Answer 1 · 2012-02-16

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12.7 years ago

Nick Loman ▴ 610

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/

ADD COMMENT • link 12.7 years ago by Nick Loman ▴ 610

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

ADD REPLY • link 12.7 years ago by Mat ▴ 50

score 2 · Answer 2 · 2012-02-16

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12.7 years ago

Pasta ★ 1.3k

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:

alt text

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 !

alt text

Believe me, biologists love this kind of representation !

ADD COMMENT • link 12.7 years ago by Pasta ★ 1.3k

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

ADD REPLY • link 12.7 years ago by Mat ▴ 50