genome and contig increased

[zhangkaihui1]

Thank you very much for your suggestion. We only used hifi data, and after adding the -l 0 parameter, the result showed that the genome was 10M in multiple places and contig increased. Based on this result, we added the - s 0.35, -D 10 and -N 150 parameters, which did not improve the result. Can you give me some advice? The species in this study was approximately 54M in size, haploid, and 50% repetitive sequence

[chhylp123]

Could you please show the contig size and N50?

[zhangkaihui1]

Could you please show the contig size and N50?

result of parameters (-s 0.1 -D 5 -N 90 and -n 10) sum = 53284092, n = 348, N50 = 196373, n = 86 N90 = 81366, n = 252 N_count = 0 Gaps = 0

result of parameters (-l 0 -s 0.1 -D 5 -N 90 and -n 10) sum = 58297740, n = 440 N50 = 172759, n = 108 N90 = 71369, n = 321 N_count = 0 Gaps = 0

result of parameters (-l 0 -s 0.1 -D 5 -N 90 and -n 11) sum = 51600902, n = 385, N50 = 175029, n = 96 N90 = 75948, n = 281 N_count = 0 Gaps = 0