merging of two assemblies from different short-reads techniques

Question

[Andrew Yu]

Hi all!

I have two data sets for one metagenome sample:

1. Illumina 2x300 bp shotgun metagenome library.
2. DNBSEQ 2x100 bp shotgun metagenome library.

THe question is: is it possible to get more deep and complex assembly by combining those datasets before\after assembly step?

I've tried just merge forward and reverse reads from both Illumina and DNBSEQ into mergred_forward.fastq and mergred_reverse.fastq and pass it to SPAdes or megahit. But I feel this is wrong approach. I figured out that genes of 16S rRNA look more accurate from separated assemblies than from merged.

Also I've heard about unicycler but it needs long-read sequencing data which i haven't. also I thought about using assembled contigs of Illumina or DNBSEQ data as pseudo-long-reads and pass to unicycler but it seems illegal.

So I'm cunfused and need some advice at this point.

Thanks a lot!