Avoid genome circularization with Canu assembler
I am doing a denovo assembly with ONT and Illumina reads, for that I'm using Canu assembler first and then, polishing with Illumina reads. The genome has some repetitive regions in both ends, and Canu assembler creates a circular genome. The genome is lineal, and the problem that I found is that there is one region at the beginning of the genome that is not assembled, it seems the reads are collapsed in other region of the genome (I saw that in IGV). My question is if there is any option in Canu or other long reads assemblers that avoid the circularization of genomes when they are assembled. Thanks!
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