Seeking Guidance on Achieving Chromosome-Level Assembly for Insect Genome

Question

[Dragn]

Dear all,

I have a HiFi sequencing (long read) and contig-level assembly of an insect (de novo whole genome assembly). Unfortunately, I don't have a reference genome in NCBI for the same species, and the available scaffold-level assemblies aren't sufficient.

I'm searching for a chromosome-level assembly to perform reference-guided assembly. How should I proceed to achieve chromosome-level assembly with my current data?

I am unsure about the next steps for working with this contig-level assembly. Any guidance to help me complete my study would be greatly appreciated.

Answer 1

[shelkmike]

Currently, the most popular way to make a chromosome-level assembly from contigs is to use a scaffolder which utilizes Hi-C reads (for example, YaHS https://github.com/c-zhou/yahs). Scaffolding using a genome of another species is dangerous, because there may be structural differences between genomes of different species.

[Dragn]

Thank you for your insights. Any suggestions on what I should do next with this HiFi reads data? My boss provided me with the data, which was assembled using the de novo assembly method wtdbg2, resulting in 1,558 contigs. I'm uncertain about the conclusions I should draw from this data. wtdbg2 assembly summary.

[shelkmike]

N50 is rather low. I suppose, if you assemble the genome using Hifiasm instead of Wtdbg2, the assembly might be better.
After you assemble a genome, there are a lot of things that you can do. First and foremost, analyze the assembly by BUSCO and estimate how many haplotypic duplications there are. Recently I published an article about the genome of Heracleum sosnowsky (https://pubmed.ncbi.nlm.nih.gov/37846604/). From the supplementary materials of this article you may see what I consider good practices of genome assembly quality control and postprocessing.

[Dragn]

Very nice and useful article and I can try the supplementary information as manual. Hope you receive my detailed message.