I am dealing with a complex plant genome (higly heterozygous, haploid genome size 2.5 Gb, I have a diploid assembly of 5 Gb, N50 200 kb, N90 5 kb) and I would like to extend its contiguity with ONT reads.
I thought of using the assembly (has scaffolds, but only 1.5% Ns) as anonther input with the ONT data in the minimap stage, to create extensions of the scaffolds. The ONT data (20x of 5 Gb, N50 9 kb) could be selected to have reads only above 2 kb, for example.
My question is whether the minimap2 alignment or graph construction steps will be affected by having two types of data: highly-accurate scaffolds and ~85% accurate ONT reads. Do you think this will be a good strategy?
Basically, the scaffolds (highly accurate at the nt level, but of coverage 1x) will be a baseline set of sequences to be extended with the longer (with coverage) ONT reads.
Do you think it is worth a try?
Thanks,
Hello,
I am dealing with a complex plant genome (higly heterozygous, haploid genome size 2.5 Gb, I have a diploid assembly of 5 Gb, N50 200 kb, N90 5 kb) and I would like to extend its contiguity with ONT reads. I thought of using the assembly (has scaffolds, but only 1.5% Ns) as anonther input with the ONT data in the minimap stage, to create extensions of the scaffolds. The ONT data (20x of 5 Gb, N50 9 kb) could be selected to have reads only above 2 kb, for example.
My question is whether the minimap2 alignment or graph construction steps will be affected by having two types of data: highly-accurate scaffolds and ~85% accurate ONT reads. Do you think this will be a good strategy?
Basically, the scaffolds (highly accurate at the nt level, but of coverage 1x) will be a baseline set of sequences to be extended with the longer (with coverage) ONT reads. Do you think it is worth a try? Thanks,
Dario