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Old 12-05-2010, 09:59 PM   #1
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Location: japan

Join Date: Oct 2010
Posts: 3
Default Scaffold using Phusion assembler

We have contigs made by velvet and minimus formatted by fasta. And we have long-inserted(2k) Mate-paired short reads generated by illumina IIx.

We want scaffold these contigs with the Mate-paired read using Phusion. But I can't understand how to use Phusion. I have been succeed in the example data assembly. But these example reads are fastq format. We must exchenge our fasta contigs to fastq format?

fasta2fastq command occured segmentation fault. It must because our Linux System(RHEL5, or CentOS5).

So we made perl script that adding quality line to fasta. It looks like fine.

And what can we do?
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