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Old 06-15-2011, 07:23 AM   #1
Location: konstanz

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Posts: 10
Default Bambus for scaffolding big genome??


I am using Bambus (version 2.33) for scaffolding our 1.1 G genome. Before using the Bambus for our data, I first tested the Bambus with the test data in the Bambus package and everything was fine.

However, Using Bambus for our data, it always crashed at the step 400, and reported that the Grommit script failed. Someone in the Abyss discuss group mentioned that Bambus is incapable of scaffolding genomes > 100 M. But, I am not sure this is the reason for our data?

My question is that dose any one has the experience of scaffolding big genome (here I mean >1 G bp genome) by Bambus?

Shaohua is offline   Reply With Quote
Old 06-21-2011, 11:18 AM   #2
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Location: United States

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Sadly I am getting the same error with a genome in the 400 MB range.

Using only a subset of sequencing runs, I got wonderful scaffold outputs from bambus, measurably larger than output from sspace or Sopra. However, the over size was only a fraction of the genome.

But I too get the grommit script error when attempting the large contig datafile.
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Old 06-23-2011, 09:46 AM   #3
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Did you find any solution for the failure of Bambus version 2.33 for scaffolding larger geomes. I am getting failure at Grommit script too.

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Old 06-25-2011, 09:41 AM   #4
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Location: Cambridge, England

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I found bambus too painful to use, so I'd recommend sspace.

Can you post your usage pipeline here?

I'd recommend contacting the bambus (amos) mailing list with your questions:
Homepage: Dan Bolser
MetaBase the database of biological databases.
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