I'm working on the assembly of a plant genome. I have 10X genomics reads (coverage: 60x) and Illumina PE (coverage: 60x).
I've tried to do the assembly with Supernova (10X genomics software and it worked fine). I've got 47000 scaffolds and N50 around 50000.
I would like to improve my results and I have assembled two addictional genomes using soapdenovo2: the first using only the Illumina PE sequences and another using the Illumina PE sequences and the 10X reads without the linker. I've made those two assembly in order to try to scaffold them with the scaffolders that use 10X linkers. I've tried ARKS, ARCS and Scaff10x, but no improvement occurs. I've also tried to raise the N50 merging the assemblies (with CISA and GARM) and scaffolding after that: not a single improvement.
Now I ran out of ideas and I would like to know if somebody knows how I can improve my assembly.
Thank you in advance