I have been trying to assemble a genome that, based on flow cytometry, should be between 1.2 to 1.5 GB. I have Illumina (more than 100x), Pacbio (50x) 10x and Hic reads. The bests assembly that we have got so far is 450 MB and 93 percent complete. It seems that the assembly collapses despite having all the newest sequencing technology data. We have tried CANU, MASURCA, FALCON, SuperNova, and MINIassem. I should mention that the flow cytometry suggests that the genome is a diploid but bioinformatic analysis suggests both diploid and tetraploid. So, my question is, does anyone have any idea why the genome assembly collapses and is there any assembly software available which can handle all these different types of reads and perform better assembly which I might not be aware of? Any suggestions and directions are greatly appreciated.
All the bests, Pezhman Safdari