Bambus for scaffolding big genome??

shaohua.fan · 06-15-2011, 07:23 AM

Hi,all,

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

fishinabarrel · 06-21-2011, 11:18 AM

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.

schamala · 06-23-2011, 09:46 AM

Hi Shaohua.fan,

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.

Thanks,
Sschamalla.

dan · 06-25-2011, 09:41 AM

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:

http://sourceforge.net/mail/?group_id=134326

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
how to use bambus for scaffolding?	elisadouzi	Bioinformatics	3	05-31-2013 03:07 PM
RNA-Seq: Scaffolding a Caenorhabditis nematode genome with RNA-seq.	Newsbot!	Literature Watch	0	10-29-2010 03:00 AM
Bambus mate file	coldturkey	Bioinformatics	7	10-16-2009 07:17 PM
Bambus	coldturkey	Bioinformatics	2	10-15-2009 06:51 AM
Instructions for scaffolding MIRA 454 contigs & 25 KB paired-end data with BAMBUS	edge	Bioinformatics	1	09-30-2009 02:04 AM

06-15-2011, 07:23 AM	#1
shaohua.fan Member Location: konstanz Join Date: Feb 2009 Posts: 10	Bambus for scaffolding big genome?? Hi,all, 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

06-25-2011, 09:41 AM	#4
dan wiki wiki Location: Cambridge, England Join Date: Jul 2008 Posts: 266	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: http://sourceforge.net/mail/?group_id=134326 __________________ Homepage: Dan Bolser MetaBase the database of biological databases.

06-21-2011, 11:18 AM	#2
fishinabarrel Junior Member Location: United States Join Date: Apr 2011 Posts: 6	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.

06-23-2011, 09:46 AM	#3
schamala Junior Member Location: Florida Join Date: Dec 2010 Posts: 1	Hi Shaohua.fan, 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. Thanks, Sschamalla.