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MariaNattestad / Assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
http://assemblytics.com
MIT License
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Identification of tandem duplications #34

Closed MehmetGoktay closed 4 years ago

MehmetGoktay commented 4 years ago

Hi Maria,

thanks for this wonderful tool.

I was just wondering , would it be possible to interpret tandem expensions as tandem duplications?

Because basically it should look like an insertion event in query sequence between alignments.

Best Regards, Mehmet

MariaNattestad commented 4 years ago

Yes a tandem duplication would fall under the category of a tandem expansion. I used "tandem expansion" because it is more general. Since the delta file uploaded to Assemblytics doesn't actually contain the base sequences, Assemblytics doesn't have the power to analyze the repeat structure directly. In the paper in figure 1A, the diagram for "tandem expansion" includes some sequence in the middle, which could be an insertion of new sequence in between the duplicated sequence. In that kind of example, calling it a tandem duplication might oversimplify it a bit, so I went with a more general term to encompass those cases as well.