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Can I detect structural variation (SV)?
Can I detect structural variation (SV)?
Updated over a week ago

Yes, Nanopore reads are ideal for the detection of structural variation, and there are a number of ONT workflows and third-party tools available for this process.

Our recommended best practice workflow is described on our Applications page and also implemented through both of our analysis platforms, EPI2ME Agent and EPI2ME Labs.

Structural variants (also known as SVs) are typically identified after the alignment of reads against a reference sequence. The resulting aligned read data (typically in BAM format) are used as input and a variant call format (VCF) file is generated containing variant predictions against this reference sequence.

For third-party tools, please see their GitHub pages for installation and usage. To address any issues with these and other third-party tools, please post to the Issues tab on the individual GitHub repositories as we cannot offer support for third-party software.

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