Understanding the results after JuiceBox

[Krešimir Križanović]

Hello,

I'm assembling a large plant genome (4.1Gbp estimated size).

I've done an initial assembly from PacBio HiFi reads using hifiasm, and then ran 3d-dna pipeline. I've loaded the FINAL.assembly file final.hic files into the JuiceBox and manually rearranged the contigs to get the best heatmap I could. This resulted in 13 chromosomes (that is the expected number).

Before JuiceBox, my N50 measure was about 100Mbp.

After manual editing with JuiceBox, I've generated a new FASTA file (as per instructions in the Genome Assembly Cookbook). The N50 measure of the assembly is about 200Mbp.

I was not expecting the N50 to change, thinking that all I did was change the order of contigs and their grouping into chromosomes.

Can you tell me if this N50 increase should happen or not?

Best regards,

Krešimir Križanović

[Olga Dudchenko]

Hello Krešimir,

1) FINAL.assembly is not the right file for manual editing. The suffixes should match, i.e. the assembly file to load with the final.hic is final.assembly. Note that FINAL.assembly has been renamed to _HiC.assembly is later releases of 3D-DNA.

2) Look into the difference between contig and scaffold N50. I am assuming the 200Mb N50 is the scaffold N50.

Olga