De novo genome assembly
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10 weeks ago

Howdy,

I have recently been tasked as the 'bioinformatics guy" in my lab and am having trouble with a de novo genome assembly of Mother of a Thousand. I am working with Nanopore reads and have ran my reads through CANU. I have all of this great data and am not sure where to go next with my work flow. Do I need a reference genome to use MiniMap2?

De novo Assembly Genome Minimap2 Mother • 396 views
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What do you want to do with minimap2? Do you only want to assemble the genome, or is something else planned? How high is your coverage?

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The plan is to first assemble the genome, then annotate. I want to then process my reads for RNAseq analysis. The coverage is 100X.

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For this, you may be better off with a de novo transcriptome assembly though. Kalanchoe daigremontiana is a descending tetraploid, right? In that case, it should be alright, because the WGD would be rather old.

For genome assembly, it's best to go with the advice by @samuel.a.odonell. Your coverage sounds great actually. However, I'm not aware of any tool for cDNA-based polishing of genomic nanopore reads. If your goal is gene expression profiling, just keep the de novo option in mind - it works fairly well in my experience.

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Do I need a reference genome to use MiniMap2?

Yes you would need a reference genome or transcriptome since minimap2 is an aligner. What kind of data do you have? RNAseq or DNAseq?

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What is your species etc? Regardless, the first thing you will want to do after nanopore assembly with canu is some long read polishing. Racon followed by medaka works well. Then short read polishing with illumina data if you have it. Then it could be refined depending on whether there is another reference genome for your species or a close species. If so you could perform scaffolding which lay then use minimap to align the assemblies

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