First of all, thank you very much for developing this tool – it's super powerful!
With only ONT ultra-long reads and Hi-C reads, it assembled two haplotypes, one of which contains only 2 gaps.
Everything is perfect, except that the gaps are too long for my concern: one gap is nearly 150 kb and another is more than 400 kb.
h1tg000022l 24804852 24953925 149074
h1tg000030l 29066927 29473287 406361
Is this a problem for gap filling? How can I solve it?
The command I used is shown below:
hifiasm --ont -t 30 --hg-size 1.88g --dual-scaf --telo-m CCCTAAA --h1 /nfs2/local/BA1_HiC_R1.fq.gz --h2 /nfs2/local/BA1_HiC_R2.fq.gz -o BA1_hifiasm_ont /nfs2/local/BA1_ONT.fq.gz
First of all, thank you very much for developing this tool – it's super powerful!
With only ONT ultra-long reads and Hi-C reads, it assembled two haplotypes, one of which contains only 2 gaps.
Everything is perfect, except that the gaps are too long for my concern: one gap is nearly 150 kb and another is more than 400 kb.
h1tg000022l 24804852 24953925 149074
h1tg000030l 29066927 29473287 406361
Is this a problem for gap filling? How can I solve it?
The command I used is shown below:
hifiasm --ont -t 30 --hg-size 1.88g --dual-scaf --telo-m CCCTAAA --h1 /nfs2/local/BA1_HiC_R1.fq.gz --h2 /nfs2/local/BA1_HiC_R2.fq.gz -o BA1_hifiasm_ont /nfs2/local/BA1_ONT.fq.gz