First of all, according to the Minia manual (and my experience) you don't need to reverse-complement any reads, and you can can feed paired reads to Minia as is - you are correct, though, Minia won't use paired-end information at all..
What do you mean by:
But the result is worse in comparison to using just one of the two.
Is it more contigs? Worst N50? Worst BUSCO score? Worst alignment against a reference genome? How much worst? What is the estimated genome size and what is the sequencing coverage? What is the sequencing technology and read length? Did you try to assemble with R1 and with R2 reads, and both assemblies were better than with R1+R2?
I think you question lacks important information for a proper answer (such as the questions above, or Minia version, or the command used), so I will provide some tentative explanations.
One possible explanation is you have too much sequencing coverage, and several assemblers have degraded performance with too much data, as there are too many sequencing errors introduced (see, e.g., When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality).
Another explanation is your R2 reads have lower quality, and when you assembly with just higher quality R1 reads, the resulting assembly will be better.
Some other comments:
Minia can handle multiple files, you don't need to concatenate them (see Multipe Files under 5 Input for instructions)
The first sentence from Minia github repository is:
If you are looking to do high-quality genome or metagenome assemblies, please go here: https://github.com/GATB/gatb-minia-pipeline
modified 8 days ago
8 days ago by
h.mon ♦ 29k