I need to assemble haploid fungus "A" using Illumina pair-end data. There are reference genomes of another two fungi (Refseq 1 and 2) isolated from a different host. I have checked the similarity between the Fungi A with Refseq 1 and 2 using DArT which is around 50%. Ref seq 1 and 2 are around 60% similar to each other.
So to assemble the data of Fungi A, I am thinking of using reference assisted denovo assembly.
My steps are as follows:
- Map Fungi A with Refseq1 using Bowtie 2
- After mapping, take unaligned reads of Fungi A and map with Refseq2
- And for remaining unaligned reads, perform denovo assembly using Spades.
So I have two questions
Is this a good approach? Or it is better to do denovo assembly of Fungi A first and later align with Refseq 1 and 2? In the latter case, which assembly tool should I used to align denovo assembled Fungi A to Refsequences?
If I use the reference assisted denovo assembly method, which tools can I used to stitch together contigs/supercontigs, close gaps to create a reference genome for fungi A.