Merging Velvet Assemblies

Sure. Get me your email address and I'll send them.

[kbushley]

Thanks, I was reading up on that one today. Would you be willing to share your script that parses MUMmer output...that sound rather useful. Go Beaves -.

Hi kbushley,

I've been using Minimus2 and am somewhat satisfied. I haven't tried CAP3 yet. I'm at the University of Oregon. Go Ducks!!!

Best,
Mike

[kbushley]

Hello Mike,

I'm also trying to do this. I think CAP3 might be the best tool but am still exploring this...there is a guy in our department who's written a program using CAP3 to merge velvet and abyss assemblies. It might be of some use. Let me know if you've found any other solutions. You also are in the great state of Oregon...where are you located?

[siiner]

I found some tools can do this job, such as CAP3, Phrap, CA, and MAIA.
But I didn't actually make any of them work well.
Hope you could try and show your results.

Hi,

This is my first post, and I look forward to being part of the community.

I've been prepping, sequencing, and assembling pools of ~10 BAC clones using PE100 reads on an Illumina. The average clone size is ~150 kb, but they can range from 50-250 kb. During the preps, I pooled an equal weight of DNA for each BAC clone, so I expect different levels of coverage from each BAC. I know that Velvet produces optimal assemblies with a k-mer coverage of 20-30X, and k-mers of ~55 give me an average coverage of that level. However, large BACs will have <20X coverage and small BACs will have >30X with this k-mer. To deal with this, I've been running Velvet with a series of k-mers (31, 41, ..., 81), and my plan is to merge the contigs from the series of assemblies.

Initially, I just used Mummer to align the contigs produced from each assembly to the other assemblies, and I wrote a script to parse the Mummer output and discard contigs that are nested within larger contigs. This works OK, but I'm looking for something more sophisticated. Does anybody have suggestions of the best software for doing this merging. What I want to do is quite simple, but I'm just not sure of the best software to use.

Thanks,
Mike