I would like to use some long reads from new nanopore data to lengthen and bridge scaffolds in an existing genome release. Does anyone have a recommendation for an assembler that would work well or is built for this task and tolerate (or preferably fill in) the NNNNs in the existing scaffolds?
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Typically due to high error rate you have to correct your nanopore reads by more accurate short reads
Alternatively, depending on how big your genome is, you could do another de-novo assembly from scratch using Canu. People have been quite successful with Nanopore assemblies of bacterial and yeast genomes using Canu.
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canu http://biorxiv.org/content/early/2016/08/24/071282
canu can assemble mammalian genome with cheap ws. https://arxiv.org/abs/1703.10231
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