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.
- 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.
- Is aligning to the reference genome using nucmer necessary, or can I skip that?
- 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 ?
Assemble with SPADES - Create scaffolds with ? -> Close gaps with ?
(Or combine the last two steps if a single program does both)
Thanks in advance!