I have a bacteria sample, and I have done genome assembly and now have its original sequence. Since the bacteria sample has come from the soil, it contained two closely related bacterias. How can I use the reference genome that I now have to assemble the "other" genome? Which programs can be helpful?
Here's what I did: I mapped my initial reads back to the contigs generated by Velvet (using BWA), then I had a look at it using Tablet. Then finally I used the SAM file generated by BWA and the contigs file I had (as reference) and the Columbus package of Velvet to generated a "hopefully" related sequence to my bacteria. I just have to mention that this task is not really biologically sound and was just a warm-up exercise I got myself involved in!