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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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. -
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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The immune system’s power comes from its genetic diversity, allowing myriad threats to be neutralized through first recognizing foreign antigens. That diversity is also what makes the immune system so difficult to study. Recent advances in sequencing technology and computational biology, however, are giving researchers new tools to understand immune responses and immune-related diseases in greater detail.
This convergence of genetics, immunology, and computation...09-01-2026, 05:41 AM
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