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aeeckhou / shallowHRD

This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination Deficiency of a tumor based on the number of Large-scale Genomic Alterations (LGAs).
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how to use it to detect genome homologous recombination in non-human resequsing data? #8

Closed Yixiangzhang1996 closed 1 year ago

Yixiangzhang1996 commented 1 year ago

how to use it to detect genome homologous recombination in non-human resequsing data?

aeeckhou commented 1 year ago

Hello,

Sorry I do not know much about Homologous Recombination Deficiency outside of human and PDX models and its exact consequences on different organisms genome. I wouldn't be able to help you and shallowHRD was not developed to assess such thing. There seems to be a lot of literature however available, notably for plants, if you want to dive into it!

Best regards, Alexandre Eeckhoutte