minimap2 + miniasm + racon pipeline produces bigger genome assembly than expected

[MehmetGoktay]

Hi,

I have assembled one plant genome which was assembled before and assembly size were 120mb. I have assembled the same genome with minimap2 + miniasm + racon pipeline but final assembly size is 131 mb. (nanopore, 30x coverage and smallest read length was 10kb)

does any one have any idea why I m getting bigger final assembly than expected?

Best,
Mehmet

[dcopetti]

Hi,
Can it be that your genome is heterozygous?
In that case, highly divergent allelic regions will be assembled on separate contigs, increasing the total size of the assembly to some value larger than the genome size.
Also, is your genome size estimation correct? If you have some Illumina data (>20x, WGS) you could run a k-mer analysis (Jellyfish, Genomescope) and see which value you get.