General Context: With the emergence of third-generation sequencing (e.g. PacBio and Oxford Nanopore), new callers have been developed that can process long-reads to detect large structural variations. Before long-read sequencing, these were difficult to detect since they often exceed the length of a short-read and thus rarely are completely covered by a single short-read. Especially the detection of copy number variations (CNVs) suffers from this circumstance.
Tool Description: However, long-read callers are susceptible to the inferior quality of long-read data. Therefore, iGenVar aims to combine long- and short-reads to guarantee better quality and the ability to call large SVs (CNVs included), as well as smaller indels, and even SNPs.
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