Closing Gaps in Illumina reads using a reference genome?

Question

[mwidel]

Hi --

I'm new to sequencing and I have a few genomes that I'm trying to close gaps in. They're all Illumina paired end reads, which I have assembled using SPADES. I've also aligned the contigs to a reference genome using nucmer.

Three questions:

1. What program can I use to close the gaps in the assembly while using a reference genome? The programs I've seen (IMAGE, SOAPdenovo2, etc.) seem to do it without a reference genome.
2. Is aligning to the reference genome using nucmer necessary, or can I skip that?
3. Do all of the gap closing softwares produce scaffolds, like SOAPdenovo2 does? Or is that a separate step?

Essentially, should my workflow go:

• Assemble with SPADES -> Align contigs to reference genome with nucmer -> Create scaffolds with ? -> Close gaps with ?

  OR

• Assemble with SPADES - Create scaffolds with ? -> Close gaps with ?

  (Or combine the last two steps if a single program does both)

Thanks in advance!