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Chromosome-scale genome assembly is affected by scaffolding errors and may yield incorrect chromosome sizes. Today, we present 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.
Demonstrator: Napari-KICS
Speaker: Arne Ludwig
Date: October 27th 2022, 1 p.m. – 2 p.m.
Location: APB-1020, Andreas-Pfitzmann-Bau (APB), Nöthnitzer Str. 46, Dresden
Information: Know your chromosome sizes: a guide to karyotype-based validation of de novo assemblies.
Application: https://github.com/mpicbg-csbd/napari-kics
This event is limited to 20 participants.
Get more information on the event: https://scads.ai/living-lab-en/living-lab-hands-on-demonstrator-series/ahttps://scads.ai/living-lab-en/living-lab-hands-on-demonstrator-series/3-napari-kics/
Find out more about the Hands-On Demonstrator Series: https://scads.ai/hands-on-demonstrator-series/
Contact:
Neringa Jurenaite
neringa.jurenaite@tu-dresden.de
Apurv Deepak Kulkarni
apurv.kulkarni@tu-dresden.de