I am working on assessing the genome I assembled with Hifiasm. The genome size estimate with flow-cytometry of the target plants I am working on is around 120Mb. The assembled genome size with Hifiasm is 272Mb.
I suspect there could be several things going on with my data: 1) This genome is super heterozygous, the assembled genome is from two very divergent haplotypes. 2) The genome sequence we obtained were from multiple individulas. 3) There might be cross-contamination from other samples during sequencing procedures. I am trying to figure out what is exactly going on and run some of those k-mer analysis to see whether it could provide any insights.
Here I attach 3 plots and the log files.
1) The plots for bot k-mer distribution of this sample
2) The GC KAT contig length and duplication plot
3) Comparison between the reads and the assembly
Thank you guys for making this amazing tool available and we have benifited from it a lot! I would really appreciate it if you could provide any insights on how to inteprete those plots. Thank you a lot.
Hi,
I am working on assessing the genome I assembled with Hifiasm. The genome size estimate with flow-cytometry of the target plants I am working on is around 120Mb. The assembled genome size with Hifiasm is 272Mb.
I suspect there could be several things going on with my data: 1) This genome is super heterozygous, the assembled genome is from two very divergent haplotypes. 2) The genome sequence we obtained were from multiple individulas. 3) There might be cross-contamination from other samples during sequencing procedures. I am trying to figure out what is exactly going on and run some of those k-mer analysis to see whether it could provide any insights.
Here I attach 3 plots and the log files. 1) The plots for bot k-mer distribution of this sample 2) The GC KAT contig length and duplication plot 3) Comparison between the reads and the assembly
sorg_k27.pdf sorg_k27_cold.pdf sorg_comp_fq_assem-main.mx.density.pdf
nohup1.txt nohup2.txt nohup3.txt
Thank you guys for making this amazing tool available and we have benifited from it a lot! I would really appreciate it if you could provide any insights on how to inteprete those plots. Thank you a lot.
Cheers Qiuyu