Oxford Nanopore Technologies

Yes, there is a number of tools available for SNP and indel detection from ONT read data. Benchmarked workflows are available from our <a href="https://nanoporetech.com/applications" rel="nofollow noopener noreferrer" target="_blank">Applications page</a> and also described in <a href="https://labs.epi2me.io/wfindex/" rel="nofollow noopener noreferrer" target="_blank">EPI2ME Labs workflows</a>.

We suggest using these resources to identify recommended workflows. Benchmarked results for SNP and indel detection are available from our <a href="https://nanoporetech.com/accuracy" rel="nofollow noopener noreferrer" target="_blank">accuracy page</a>.

SNPs and indels 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.)

Can I detect SNP/indels (insertions and deletions)?

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