assembly tool for plant data

Question

[analyst]

I have to generate assembly of polyploid and aneuploid sugarcane wgs data. I have only short reads. Can you please suggest any short read assembly tool compatible for polyploid data?

Also annotation tool. I need to annotate the assembly afterwards.

Thanks

Answer 1

[colindaven]

I don't think that's possible - or if it is possible, it will not be satisfactory, informative or publishable. In short, sugar cane is one of the hardest plant genomes around and it is likely a huge amount of work even with all required data.

I would use a modern, Pacbio Hifi or ONT assembled genome with Hi-C like this https://www.nature.com/articles/s41467-024-47390-6 and align your short reads to it.

I would also try to educate your PI about genomics and realism.

[Dave Carlson]

This is exactly right. It will not be a productive use of your time to try to assemble any polyploid plant genome with only short reads.

[analyst]

Right collindaven!

My PI is from agricultural wet lab background. He provided me one WGS sample with 100x coverage to find variety specific novelty through assembly and variant calling.

I called variants from chromosime-wise splitted bam files (since original file was large in size so splitted the bam file chromosome-wise). Haplotypecaller was used setting ploidy 12. Please also correct if it is right approach to set ploidy 12 since it is aneuploid data.

Now second part was performing assembly.

Please guide what useful analysis can i perform with this kind of data.

Thanks alot