Demonstrator: Napari-KICS
Speaker: Arne Ludwig
Date: October 27th 2022, 1 p.m. – 2 p.m.
Location: ScaDS.AI Living Lab (APB-1020), Andreas-Pfitzmann-Bau (APB), Nöthnitzer Str. 46, 01187 Dresden, Germany
Know your chromosome sizes: a guide to karyotype-based validation of de novo assemblies.
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Chromosome-scale genome assembly is affected by scaffolding errors and may yield incorrect chromosome sizes. Today, we present Napari-KICS, a semi-automated and cost-efficient approach for examining the validity of the assembly by estimating relative chromosome sizes from the respective karyotype images. The method employs threshold-based image segmentation and uses the extracted chromosome areas as proxies for the actual chromosome sizes. The suitability of the approach is confirmed by a strong correlation between area and DNA content evaluated on karyotype images of varied species and achieving a 6 Mb chromosome size error on a reference human karyotype dataset.
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