rate Ask for help! how to integrate BAC scaffolds and Illumina Data

[wzhangvv]

Hi All,

This is my first time to do de novo genome assembly for a specific region. Now I have assembled BAC scaffolds and I also assembled illumina short reads to scaffolds using SGA assembler. Then I want to use scaffolds from the short reads to fill the gaps among BAC scaffolds. Do you guys have some idea to recommend a software for me?
Thank you so much!

Wei

[jimmybee]

You could use another assembler like Phred/Phrap. There should be a few threads on the site where people have used different programs for scaffolding. Have a bit of a dig around in the similar threads