Assembly-Based Inversion Calling

Posted on Tue 11 September 2018 in genomics • Tagged with genomics, structural variantsLeave a comment

Both WGS alignment methods and whole genome alignment methods are used to computationally identify structural variants (SVs). Assemblytics is an example of a whole genome alignment method, as it scans nucmer alignments of a query genome to a reference genome to call variants. However, Assemblytics only calls insertions and deletions (and expansions and contractions, but we can consider those insertions and deletions respectively). In an effort to expand this software, I want to add the ability to call more types of variants such as inversions and translocations. Here, I focus on inversions and begin to investigate how very simple inversions appear in genome-genome alignments.

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