can specific haploid parameters be added to improve assembly results?

[zhangkaihui1]

Hello, the species I studied is haploid. After using hifiasm software to assemble hifi and ont data, the test.bp.p_ctg.gfa results showed that the genome size was correct and there were more contig. Given that hifiasm is a diploid species software, can specific haploid parameters be added to improve assembly results?

[chhylp123]

It would be better to use -l0 which is develped for haploid assembly.

[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

[zhangkaihui1]

Thank you very much for your suggestion. We only used hifi data, and after adding the - l 0，the result showed that the genome was 10M in multiple places and contig increased. Based on this result, we added the -s 0.35 -D10 and -N150 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. | | zkh15886723100 | | ***@***.*** | ---- Replied Message ---- | From | ***@***.***> | | Date | 09/03/2023 21:02 | | To | chhylp123/hifiasm ***@***.***> | | Cc | zhangkaihui1 ***@***.***>, Author ***@***.***> | | Subject | Re: [chhylp123/hifiasm] can specific haploid parameters be added to improve assembly results? (Issue #516) | It would be better to use -l0 which is develped for haploid assembly. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>