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Old 12-17-2010, 02:14 AM   #1
Location: shanghai, chia

Join Date: Mar 2009
Posts: 67
Default export scaffold or link information

I have got about 189 contigs from velvet by assembling 75 bp pair end sequence. Now, i get some 3k mate pair sequence, and align with the contigs. I'd like to know if there is some software can help to export scaffold or link information between the contigs.
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Old 12-17-2010, 06:50 AM   #2
Location: Umeň, Sweden

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I have used SSPACE with nice results (Boetzer et al. 2010). You could also look at Bambus but it is a little bit more complicated to set up.
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Old 12-19-2010, 11:39 PM   #3
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Location: NL, Leiden

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thanks Andreas for using my software package. You can indeed scaffold your Velvet contigs with SSPACE. For best results, use both pair-end and mate pair sequences.

Have a look at this thread anyone1985;

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