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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Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
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