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
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
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