Hello
I'm currently assembling a diploid fungal genome using hifiasm and Hi-C ont hifi data. After analyzing the data with juicer and applying 3d-dna, I've discerned the structure of two chromosomes:
Chr14A is composed of h1g14l fragment1 concatenated with h2g11l fragment1.
Chr14B, on the other hand, consists of H1g14l fragment12 followed by h2g11l fragment2.
My question is regarding the next steps in my workflow:
Should I dismantle these chromosomes based on the fragments identified and subsequently employ Oxford Nanopore (ONT) reads for gap filling? Or, would it be more advantageous to isolate the sequences that align specifically to Chr14A and Chr14B and carry out independent assemblies for each of these two chromosomes?
我在用hifiasm 软件利用Hic ont hifi 数据组装两个核的真菌基因组，通过juicer，3d-dna挂载发现 Chr14A：h1g14l fragment1 + h2g11l fragment1 Chr14B: H1g14l fragment12 h2g11l fragment2。那我后面是拆分后用ont 填洞，还是说提取比对到这两条染色体上的序列，然后再单独组装这两条染色体
Hello I'm currently assembling a diploid fungal genome using hifiasm and Hi-C ont hifi data. After analyzing the data with juicer and applying 3d-dna, I've discerned the structure of two chromosomes:
Chr14A is composed of h1g14l fragment1 concatenated with h2g11l fragment1. Chr14B, on the other hand, consists of H1g14l fragment12 followed by h2g11l fragment2. My question is regarding the next steps in my workflow: Should I dismantle these chromosomes based on the fragments identified and subsequently employ Oxford Nanopore (ONT) reads for gap filling? Or, would it be more advantageous to isolate the sequences that align specifically to Chr14A and Chr14B and carry out independent assemblies for each of these two chromosomes? 我在用hifiasm 软件利用Hic ont hifi 数据组装两个核的真菌基因组，通过juicer，3d-dna挂载发现 Chr14A：h1g14l fragment1 + h2g11l fragment1 Chr14B: H1g14l fragment12 h2g11l fragment2。那我后面是拆分后用ont 填洞，还是说提取比对到这两条染色体上的序列，然后再单独组装这两条染色体