Can Tgsgaploser fill gaps in the genome at the chromosome level?

[XXH123a]

Dear developer, May I ask, I am trying to use 20X HiFi reads and hifiasm. p_ utg.fa fills the gap generated by 3DDNA assembly and runs twice successfully, but 36 gaps still exist. Do you think it is necessary to adjust the parameters or do you think it is unnecessary to run tgsgapcloser? genome.updated_scaff_infos.txt [Uploading 运行的参数.txt…]()

[XXH123a]

tgsgapcloser --scaff rosa2_chr.fasta --reads rosa_HiFi_Q35_L10.fa --output rosa2 --ne --minmap_arg '-x asm20 -K 80M' --tgstype pb --thread 10 --g_check >pipe.log 2>pipe.err

tgsgapcloser --scaff rosa2_chr.fasta --reads rosa_hifiasm.p_utg.fa --output rosa2 --ne --minmap_arg '-x asm5 ' --min_match 2000 --tgstype pb --thread 20 --g_check >pipe.log 2>pipe.err

[cchd0001]

I prefer to keep those 36 gaps or solve them with other tools if TGSGapCloser already fills some of the 3DDNA gaps (I assume the number of filling gaps is more than 36 ? ). After all, a too loose parameter may induce incorrect filling sequences.

[adonis316]

We have tried to use TGS-GapCloser to generate a gap-free T2T genome in several projects. But there are always some gaps left that cannot be automatically filled using default parameters. They could be due to uneven genome coverage, repetitive regions, or telomere regions. But you can use minimap2+IGV or mummer or other software tools to manually resolve these problems. Also, longer reads such as ultra-long nanopore reads can help to close these complicated gaps.

Thanks, Mengyang

[XXH123a]

Thank you for your enthusiastic guidance. The genome I assembled with 3DDNA has generated 36 gaps. I would like to try using tgsgapcloser to create one or two gap free chromosomes, but it seems much more difficult than I imagined.