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On classification of inserted sequences

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Yuichi Shiraishi edited this page Apr 6, 2024 · 2 revisions

There are many possible types of such as:

  • Tandem duplications
  • Mobile element insertions (MEIs)
  • Viral sequence integrations
  • Processed pseudogenes.

To systematically characterize the inserted sequences with a particular focus on MEIs (because of personal interest!), we have developed a pipeline. This pipeline classifies the inserted sequences by comparing them with the transcriptome, annotating them with repeat sequence information, and re-aligning them to the reference genome. The overview of the classification pipeline is depicted below. Please refer to the nanomonsv paper for the details.

Insert_classification

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