Fungus genome assembly using two reference sequences

Question

[Barsha]

Hello,

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:

1. Map Fungi A with Refseq1 using Bowtie 2
2. After mapping, take unaligned reads of Fungi A and map with Refseq2
3. And for remaining unaligned reads, perform denovo assembly using Spades.

So I have two questions

1. 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?

2. 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.

Thanks.

[h.mon]

Reference-based assembly is intended when one has a really close reference genome, and even then it can introduce errors. If the reference is only ~50% similar to the target strain, it is better to perform de novo assembly.

[Barsha]

Thanks. Because the fungi I am trying to map are same as the reference genomes but are only collected from different host.I would like to use the two reference genomes to improve the quality of the assembly of my fungi genome. Is there a way to do that after performing denovo assembly?