I have raw reads generated from Nanopore sequencing and have already performed a de novo assembly. Now, I would like to perform a reference-guided assembly using these reads. My questions are:
What are the recommended tools for performing reference-guided assembly with Nanopore reads? Are there any specific considerations or best practices for using these tools with Nanopore sequencing data?
I think you should look into RagTag. Considerations regarding the use of reference-based correction and scaffolding depend on the field of application, the similarity and quality of the reference genome, and which ragtag steps you would like and can afford to apply. I would advise caution for over-correction. If you apply all steps, the outcome will be 99.9% identical to the reference, then, why sequence in the first place? If you want to look into structural variants or SNVs, or have haplotype-resolved assemblies, I would not apply reference-based corrections.
I would not do reference guided assembly with nanopore ( to be clear assembling reads into contigs using a related reference) and I do not know of any tools which exist.
As Michael says, instead use RagTag to map your assembled contigs to a closely related reference if you want to assemble to chromosome level.
if you consider to ignore the advice of Michael and colindaven (and their arguments why not to) , you can have a look at flye or rebaler , I think they can use a reference in the assembly process.
SPAdes also has a --known-contigs option where you can input a reference genome.
Spades has an option for Nanopore data but I haven't seen any Nanopore assembly by spades.
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version 2.3.6
ok i understand. Thank you for your suggestion.