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Old 08-19-2010, 12:50 AM   #1
Location: Australia

Join Date: Aug 2010
Posts: 54
Default How To: Contig to Scaffold?


I would be grateful to have suggestions regarding the followings:

1) I have a set of contigs from the de novo assembly of ~2GB 454Flx data using the 'newbler' assembler (version 2.0.01). This version of 'newbler' do not create any scaffold from the contigs. I just wonder what tool I may use to make scaffolds using the contigs. I have the following output files from 'newbler': 454contigs.fna, 454contigs.ace and 454contigs.qual

2) For the same species, I have contigs from the assembler 'SoapDeNovo' using Illumina paired-end reads. I just have the 'Soap_contigs.fna' contig file. I have blasted 'newbler' contigs against 'SoapDeNovo' contigs. How I may use contigs from two different platforms to make scaffolds.

Both the assemblies are done outside as we don't have in-house HPC facility. For the task described above I just have my own desktop machine (Mac OSX 10.6, 2.26Ghz Core2Duo, 4GB RAM).

Thanks in advance for any help.

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