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Plasmid assembly of Oxford nanopore sequencing reads

I have the raw reads, sequencing done using Oxford nanopore platform. I want to perform whole genome and plasmid assembly from this reads. In case of illumina this job can be done by plamidspade. I need suggestion regarding the tools for performing the task and whether plasmid assembly of nanopore reads can be done using plasmidspade.

plasmid assembly nanopore oxford sequencing
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written by MG_19 • MG_19

1 answer

SPades as you mention can use Nanopore to assemble plasmids, also Flye

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written by JC JC

But it is written in the manuals that SPAdes cannot be used for only PacBio CLR, Oxford Nanopore, Sanger reads or contig sequences as SPAdes is capable of performing hybrid assemblies of short and long noisy reads, but cannot be used for long-read assemblies alone. Is there any other tools easy to run for assembly of Nanopore reads specifically plasmid assembly.

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written by MG_19 • MG_19

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